def __init__(self):
super().__init__()
self.embedders = sorted(list(EMBEDDERS_INFO))
self._image_attributes = None
self._input_data = None
self._log = logging.getLogger(__name__)
self._task = None
self._setup_layout()
self._image_embedder = None
self._executor = qconcurrent.ThreadExecutor(
self, threadPool=QThreadPool(maxThreadCount=1))
self.setBlocking(True)
QTimer.singleShot(0, self._init_server_connection)
def __init__(self):
super().__init__()
# commit
self.commit_button = None
# progress bar
self.progress_bar = None
self.progress_bar_iterations = None
# data
self.input_data = None
self.input_genes = None
self.tax_id = None
self.use_attr_names = None
self.gene_id_attribute = None
self.gene_id_column = None
self.input_info = None
self.num_of_sel_genes = 0
# filter
self.lineEdit_filter = None
self.search_pattern = ''
self.organism_select_combobox = None
# data model view
self.data_view = None
self.data_model = None
# gene matcher NCBI
self.gene_matcher = None
# filter proxy model
self.filter_proxy_model = None
# hierarchy widget
self.hierarchy_widget = None
self.hierarchy_state = None
# threads
self.threadpool = QThreadPool(self)
self.workers = None
# gui
self.setup_gui()
def __init__(self,
parent=None,
signalManager=None,
name="Databases update"):
OWWidget.__init__(self,
parent,
signalManager,
name,
wantMainArea=False)
self.searchString = ""
fbox = gui.widgetBox(self.controlArea, "Filter")
self.completer = TokenListCompleter(self,
caseSensitivity=Qt.CaseInsensitive)
self.lineEditFilter = QLineEdit(textChanged=self.search_update)
self.lineEditFilter.setCompleter(self.completer)
fbox.layout().addWidget(self.lineEditFilter)
box = gui.widgetBox(self.controlArea, "Files")
self.filesView = QTreeWidget(self)
self.filesView.setHeaderLabels(header_labels)
self.filesView.setRootIsDecorated(False)
self.filesView.setUniformRowHeights(True)
self.filesView.setSelectionMode(QAbstractItemView.NoSelection)
self.filesView.setSortingEnabled(True)
self.filesView.sortItems(header.Title, Qt.AscendingOrder)
self.filesView.setItemDelegateForColumn(
0, UpdateOptionsItemDelegate(self.filesView))
self.filesView.model().layoutChanged.connect(self.search_update)
box.layout().addWidget(self.filesView)
layout = QHBoxLayout()
gui.widgetBox(self.controlArea, margin=0, orientation=layout)
self.updateButton = gui.button(
box,
self,
"Update all",
callback=self.update_all,
tooltip="Update all updatable files",
)
self.downloadButton = gui.button(
box,
self,
"Download all",
callback=self.download_filtered,
tooltip="Download all filtered files shown")
self.cancelButton = gui.button(
box,
self,
"Cancel",
callback=self.cancel_active_threads,
tooltip="Cancel scheduled downloads/updates.")
self.addButton = gui.button(box,
self,
"Add ...",
callback=self.__handle_dialog,
tooltip="Add files for personal use.")
layout.addWidget(self.updateButton)
layout.addWidget(self.downloadButton)
layout.addWidget(self.cancelButton)
layout.addStretch()
layout.addWidget(self.addButton)
# Enable retryButton once connection is established
# self.retryButton = gui.button(
# box, self, "Reconnect", callback=self.initialize_files_view
# )
# self.retryButton.hide()
self.resize(800, 600)
self.update_items = []
self._dialog = None
self.progress_bar = None
# threads
self.threadpool = QThreadPool(self)
#self.threadpool.setMaxThreadCount(1)
self.workers = list()
self.initialize_files_view()
def __init__(self, parent=None, signalManager=None,
name="Databases update"):
OWWidget.__init__(self, parent, signalManager, name,
wantMainArea=False)
self.searchString = ""
fbox = gui.widgetBox(self.controlArea, "Filter")
self.completer = TokenListCompleter(
self, caseSensitivity=Qt.CaseInsensitive)
self.lineEditFilter = QLineEdit(textChanged=self.SearchUpdate)
self.lineEditFilter.setCompleter(self.completer)
fbox.layout().addWidget(self.lineEditFilter)
box = gui.widgetBox(self.controlArea, "Files")
self.filesView = QTreeWidget(self)
self.filesView.setHeaderLabels(
["", "Data Source", "Update", "Last Updated", "Size"])
self.filesView.setRootIsDecorated(False)
self.filesView.setUniformRowHeights(True)
self.filesView.setSelectionMode(QAbstractItemView.NoSelection)
self.filesView.setSortingEnabled(True)
self.filesView.sortItems(1, Qt.AscendingOrder)
self.filesView.setItemDelegateForColumn(
0, UpdateOptionsItemDelegate(self.filesView))
self.filesView.model().layoutChanged.connect(self.SearchUpdate)
box.layout().addWidget(self.filesView)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
self.updateButton = gui.button(
box, self, "Update all",
callback=self.UpdateAll,
tooltip="Update all updatable files",
)
self.downloadButton = gui.button(
box, self, "Download all",
callback=self.DownloadFiltered,
tooltip="Download all filtered files shown"
)
self.cancelButton = gui.button(
box, self, "Cancel", callback=self.Cancel,
tooltip="Cancel scheduled downloads/updates."
)
self.retryButton = gui.button(
box, self, "Reconnect", callback=self.RetrieveFilesList
)
self.retryButton.hide()
gui.rubber(box)
self.warning(0)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
gui.rubber(box)
self.infoLabel = QLabel()
self.infoLabel.setAlignment(Qt.AlignCenter)
self.controlArea.layout().addWidget(self.infoLabel)
self.infoLabel.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
self.updateItems = []
self.resize(800, 600)
self.progress = ProgressState(self, maximum=3)
self.progress.valueChanged.connect(self._updateProgress)
self.progress.rangeChanged.connect(self._updateProgress)
self.executor = ThreadExecutor(
threadPool=QThreadPool(maxThreadCount=2)
)
task = Task(self, function=self.RetrieveFilesList)
task.exceptionReady.connect(self.HandleError)
task.start()
self._tasks = []
self._haveProgress = False
def __init__(self):
super().__init__()
self.res = None
self.organism = '44689'
self.server = 'https://dictyexpress.research.bcm.edu'
self.headerLabels = [x[1] for x in Labels]
self.searchString = ""
self.items = []
self.progress_bar = None
# threads
self.threadpool = QThreadPool()
# Login Section
box = gui.widgetBox(self.controlArea, 'Login')
self.namefield = gui.lineEdit(box,
self,
"username",
"Username:"******"password",
"Password:"******"Output", addSpace=True)
gui.radioButtonsInBox(box,
self,
"gene_as_attr_name",
["Genes in rows", "Genes in columns"],
callback=self.invalidate)
self.controlArea.layout().addWidget(h_line())
self.refresh_button = gui.button(self.controlArea,
self,
"Refresh",
callback=self.refresh)
self.handle_cache_button(True)
gui.rubber(self.controlArea)
self.commit_button = gui.auto_commit(self.controlArea,
self,
"auto_commit",
"&Commit",
box=False)
# Experiment Section
label = QLabel("Available projects:")
my_font = QFont()
my_font.setBold(True)
label.setFont(my_font)
self.mainArea.layout().addWidget(label)
self.mainArea.layout().addWidget(h_line())
self.filter = gui.lineEdit(self.mainArea,
self,
"searchString",
"Filter:",
callbackOnType=True,
callback=self.search_update)
self.experimentsWidget = QTreeWidget(alternatingRowColors=True,
rootIsDecorated=False,
uniformRowHeights=True,
sortingEnabled=True)
self.experimentsWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole))
self.experimentsWidget.selectionModel().selectionChanged.connect(
self.on_selection_changed)
self.experimentsWidget.setHeaderLabels(self.headerLabels)
self.mainArea.layout().addWidget(self.experimentsWidget)
self.auth_set()
self.connect()
self.sizeHint()
def __init__(self, parent=None):
super().__init__(parent)
self.geneMatcherSettings = [False, False, True, False]
self.data = None
self.referenceData = None
self.taxid_list = []
self.__genematcher = (None, fulfill(gene.matcher([])))
self.__invalidated = False
self.currentAnnotatedCategories = []
self.state = None
self.__state = OWSetEnrichment.Initializing
box = gui.widgetBox(self.controlArea, "Info")
self.infoBox = gui.widgetLabel(box, "Info")
self.infoBox.setText("No data on input.\n")
self.speciesComboBox = gui.comboBox(
self.controlArea,
self,
"speciesIndex",
"Species",
callback=self.__on_speciesIndexChanged)
box = gui.widgetBox(self.controlArea, "Entity names")
self.geneAttrComboBox = gui.comboBox(box,
self,
"geneattr",
"Entity feature",
sendSelectedValue=0,
callback=self.updateAnnotations)
cb = gui.checkBox(box,
self,
"genesinrows",
"Use feature names",
callback=self.updateAnnotations,
disables=[(-1, self.geneAttrComboBox)])
cb.makeConsistent()
# gui.button(box, self, "Gene matcher settings",
# callback=self.updateGeneMatcherSettings,
# tooltip="Open gene matching settings dialog")
self.referenceRadioBox = gui.radioButtonsInBox(
self.controlArea,
self,
"useReferenceData", ["All entities", "Reference set (input)"],
tooltips=[
"Use entire genome (for gene set enrichment) or all " +
"available entities for reference",
"Use entities from Reference Examples input signal " +
"as reference"
],
box="Reference",
callback=self.updateAnnotations)
box = gui.widgetBox(self.controlArea, "Entity Sets")
self.groupsWidget = QTreeWidget(self)
self.groupsWidget.setHeaderLabels(["Category"])
box.layout().addWidget(self.groupsWidget)
hLayout = QHBoxLayout()
hLayout.setSpacing(10)
hWidget = gui.widgetBox(self.mainArea, orientation=hLayout)
gui.spin(hWidget,
self,
"minClusterCount",
0,
100,
label="Entities",
tooltip="Minimum entity count",
callback=self.filterAnnotationsChartView,
callbackOnReturn=True,
checked="useMinCountFilter",
checkCallback=self.filterAnnotationsChartView)
pvalfilterbox = gui.widgetBox(hWidget, orientation="horizontal")
cb = gui.checkBox(pvalfilterbox,
self,
"useMaxPValFilter",
"p-value",
callback=self.filterAnnotationsChartView)
sp = gui.doubleSpin(
pvalfilterbox,
self,
"maxPValue",
0.0,
1.0,
0.0001,
tooltip="Maximum p-value",
callback=self.filterAnnotationsChartView,
callbackOnReturn=True,
)
sp.setEnabled(self.useMaxFDRFilter)
cb.toggled[bool].connect(sp.setEnabled)
pvalfilterbox.layout().setAlignment(cb, Qt.AlignRight)
pvalfilterbox.layout().setAlignment(sp, Qt.AlignLeft)
fdrfilterbox = gui.widgetBox(hWidget, orientation="horizontal")
cb = gui.checkBox(fdrfilterbox,
self,
"useMaxFDRFilter",
"FDR",
callback=self.filterAnnotationsChartView)
sp = gui.doubleSpin(
fdrfilterbox,
self,
"maxFDR",
0.0,
1.0,
0.0001,
tooltip="Maximum False discovery rate",
callback=self.filterAnnotationsChartView,
callbackOnReturn=True,
)
sp.setEnabled(self.useMaxFDRFilter)
cb.toggled[bool].connect(sp.setEnabled)
fdrfilterbox.layout().setAlignment(cb, Qt.AlignRight)
fdrfilterbox.layout().setAlignment(sp, Qt.AlignLeft)
self.filterLineEdit = QLineEdit(self, placeholderText="Filter ...")
self.filterCompleter = QCompleter(self.filterLineEdit)
self.filterCompleter.setCaseSensitivity(Qt.CaseInsensitive)
self.filterLineEdit.setCompleter(self.filterCompleter)
hLayout.addWidget(self.filterLineEdit)
self.mainArea.layout().addWidget(hWidget)
self.filterLineEdit.textChanged.connect(
self.filterAnnotationsChartView)
self.annotationsChartView = QTreeView(
alternatingRowColors=True,
sortingEnabled=True,
selectionMode=QTreeView.ExtendedSelection,
rootIsDecorated=False,
editTriggers=QTreeView.NoEditTriggers,
)
self.annotationsChartView.viewport().setMouseTracking(True)
self.mainArea.layout().addWidget(self.annotationsChartView)
contextEventFilter = gui.VisibleHeaderSectionContextEventFilter(
self.annotationsChartView)
self.annotationsChartView.header().installEventFilter(
contextEventFilter)
self.groupsWidget.itemClicked.connect(self.subsetSelectionChanged)
gui.auto_commit(self.controlArea, self, "autocommit", "Commit")
self.setBlocking(True)
task = EnsureDownloaded([(taxonomy.Taxonomy.DOMAIN,
taxonomy.Taxonomy.FILENAME),
(geneset.sfdomain, "index.pck")])
task.finished.connect(self.__initialize_finish)
self.setStatusMessage("Initializing")
self._executor = ThreadExecutor(parent=self,
threadPool=QThreadPool(self))
self._executor.submit(task)
def __init__(self):
super().__init__()
# commit
self.commit_button = None
# progress bar
self.progress_bar = None
self.progress_bar_iterations = None
# data
self.input_data = None
self.input_genes = []
self.tax_id = None
self.use_attr_names = None
self.gene_id_attribute = None
self.gene_id_column = None
# custom gene sets
self.custom_data = None
self.feature_model = DomainModel(valid_types=(DiscreteVariable, StringVariable))
self.custom_gs_col_box = None
self.gs_label_combobox = None
self.custom_tax_id = None
self.custom_use_attr_names = None
self.custom_gene_id_attribute = None
self.custom_gene_id_column = None
self.num_of_custom_sets = None
# Gene Sets widget
self.gs_widget = None
# info box
self.input_info = None
self.num_of_sel_genes = 0
# filter
self.line_edit_filter = None
self.search_pattern = ''
self.organism_select_combobox = None
# data model view
self.data_view = None
self.data_model = None
# gene matcher NCBI
self.gene_matcher = None
# filter proxy model
self.filter_proxy_model = None
# hierarchy widget
self.hierarchy_widget = None
self.hierarchy_state = None
# spinbox
self.spin_widget = None
# threads
self.threadpool = QThreadPool(self)
self.workers = None
self._task = None # type: Optional[Task]
self._executor = ThreadExecutor()
# gui
self.setup_gui()
def __init__(self, parent=None):
super().__init__(parent)
self.selectedDatabase = 0
self.uniqueRows = True
gui.button(gui.widgetBox(self.controlArea, "Cache", addSpace=True),
self, "Clear cache",
tooltip="Clear saved query results",
callback=self.clearCache)
self.serviceindex = 0
self.serviceCombo = gui.comboBox(
self.controlArea, self, "serviceindex", "Mart Service",
callback=self._setServiceUrl
)
for name, url in MartServices:
self.serviceCombo.addItem(name, userData=url)
idx = self.serviceCombo.findData(self.selectedService, Qt.UserRole)
self.serviceCombo.setCurrentIndex(idx)
# self.selectedService = self.serviceCombo.itemData(self.serviceCombo.currentItem())
self.martsCombo = gui.comboBox(
self.controlArea, self, "selectedDatabase", "Database",
callback=self.setSelectedMart,
addSpace=True)
self.martsCombo.setMaximumWidth(250)
self.datasetsCombo = gui.comboBox(
self.controlArea, self, "selectedDataset", "Dataset",
callback=self.setSelectedDataset,
addSpace=True)
self.datasetsCombo.setMaximumWidth(250)
gui.rubber(self.controlArea)
box = gui.widgetBox(self.controlArea, "Results")
gui.checkBox(
box, self, "uniqueRows", "Unique results only",
tooltip="Return unique results only.",)
self.commitButton = gui.button(
box, self, "Get Results", callback=self.commit,
tooltip="Query the BioMart server and output the results",
autoDefault=True)
self.commitButton.setEnabled(False)
self.mainWidget = gui.widgetBox(
self.mainArea, orientation=QStackedLayout())
self.mainTab = QTabWidget()
self.mainWidget.layout().addWidget(self.mainTab)
self.attributesConfigurationBox = gui.createTabPage(self.mainTab, "Attributes")
if self.SHOW_FILTERS: # ??
self.filtersConfigurationBox = gui.createTabPage(self.mainTab, "Filters")
self.error(0)
self.setEnabled(False)
self._task = None
self._executor = concurrent.ThreadExecutor(
threadPool=QThreadPool(maxThreadCount=2)
)
service = self.selectedService
self._task = task = concurrent.Task(
function=partial(self._get_registry, url=service))
task.resultReady.connect(self.setBioMartRegistry)
task.exceptionReady.connect(self._handleException)
self._executor.submit(task)
self._setServiceUrl()
self._afterInitQueue = []
try:
from Bio import SeqIO
self.hasBiopython = True
except ImportError:
self.warning(100, "Biopython package not found.\nTo retrieve FASTA sequence data from BioMart install Biopython.")
self.hasBiopython = False
def __init__(self,
parent=None,
signalManager=None,
name="Databases update"):
OWWidget.__init__(self,
parent,
signalManager,
name,
wantMainArea=False)
self.searchString = ""
fbox = gui.widgetBox(self.controlArea, "Filter")
self.completer = TokenListCompleter(self,
caseSensitivity=Qt.CaseInsensitive)
self.lineEditFilter = QLineEdit(textChanged=self.search_update)
self.lineEditFilter.setCompleter(self.completer)
fbox.layout().addWidget(self.lineEditFilter)
box = gui.widgetBox(self.controlArea, "Files")
self.filesView = QTreeWidget(self)
self.filesView.setHeaderLabels(header_labels)
self.filesView.setRootIsDecorated(False)
self.filesView.setUniformRowHeights(True)
self.filesView.setSelectionMode(QAbstractItemView.NoSelection)
self.filesView.setSortingEnabled(True)
self.filesView.sortItems(header.Title, Qt.AscendingOrder)
self.filesView.setItemDelegateForColumn(
0, UpdateOptionsItemDelegate(self.filesView))
self.filesView.model().layoutChanged.connect(self.search_update)
box.layout().addWidget(self.filesView)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
self.updateButton = gui.button(
box,
self,
"Update all",
callback=self.update_all,
tooltip="Update all updatable files",
)
self.downloadButton = gui.button(
box,
self,
"Download all",
callback=self.download_filtered,
tooltip="Download all filtered files shown")
self.cancelButton = gui.button(
box,
self,
"Cancel",
callback=self.cancel_active_threads,
tooltip="Cancel scheduled downloads/updates.")
# add empty label to separate button.
# TODO: is there better way of doing this?
box.layout().addWidget(QLabel(), Qt.AlignRight)
self.addButton = gui.button(box,
self,
"Add ...",
callback=self.__handle_dialog,
tooltip="Add files for personal use.")
self.retryButton = gui.button(box,
self,
"Reconnect",
callback=self.initialize_files_view)
self.retryButton.hide()
# gui.rubber(box)
self.warning(0)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
gui.rubber(box)
self.infoLabel = QLabel()
self.infoLabel.setAlignment(Qt.AlignCenter)
self.controlArea.layout().addWidget(self.infoLabel)
self.infoLabel.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
self.resize(800, 600)
self.update_items = []
self._dialog = None
self.progress_bar = None
# threads
self.threadpool = QThreadPool(self)
#self.threadpool.setMaxThreadCount(1)
self.workers = list()
self.initialize_files_view()
def __init__(self):
super().__init__()
# ATTRIBUTES #
self.target_database = NCBI_ID
# input data
self.input_data = None
self.input_genes = None
self.tax_id = None
self.column_candidates = []
# input options
self.organisms = []
# gene matcher
self.gene_matcher = None
# threads
self.threadpool = QThreadPool(self)
self.workers = None
# progress bar
self.progress_bar = None
self._timer = QTimer()
self._timer.timeout.connect(self._apply_filter)
self._timer.setSingleShot(True)
# GUI SECTION #
# Control area
self.info_box = widgetLabel(
widgetBox(self.controlArea, "Info", addSpace=True),
'No data on input.\n')
organism_box = vBox(self.controlArea, 'Organism')
self.organism_select_combobox = comboBox(
organism_box,
self,
'selected_organism',
callback=self.on_input_option_change)
self.get_available_organisms()
self.organism_select_combobox.setCurrentIndex(self.selected_organism)
box = widgetBox(self.controlArea, 'Gene IDs in the input data')
self.gene_columns_model = itemmodels.DomainModel(
valid_types=(StringVariable, DiscreteVariable))
self.gene_column_combobox = comboBox(
box,
self,
'selected_gene_col',
label='Stored in data column',
model=self.gene_columns_model,
sendSelectedValue=True,
callback=self.on_input_option_change)
self.attr_names_checkbox = checkBox(
box,
self,
'use_attr_names',
'Stored as feature (column) names',
disables=[(-1, self.gene_column_combobox)],
callback=self.on_input_option_change)
self.gene_column_combobox.setDisabled(bool(self.use_attr_names))
output_box = vBox(self.controlArea, 'Output')
# separator(output_box)
# output_box.layout().addWidget(horizontal_line())
# separator(output_box)
self.exclude_radio = checkBox(output_box,
self,
'exclude_unmatched',
'Exclude unmatched genes',
callback=self.commit)
self.replace_radio = checkBox(output_box,
self,
'replace_id_with_symbol',
'Replace feature IDs with gene names',
callback=self.commit)
auto_commit(self.controlArea,
self,
"auto_commit",
"&Commit",
box=False)
rubber(self.controlArea)
# Main area
self.filter = lineEdit(self.mainArea,
self,
'search_pattern',
'Filter:',
callbackOnType=True,
callback=self.handle_filter_callback)
# rubber(self.radio_group)
self.mainArea.layout().addWidget(self.filter)
# set splitter
self.splitter = QSplitter()
self.splitter.setOrientation(Qt.Vertical)
self.table_model = GeneInfoModel()
self.table_view = QTableView()
self.table_view.setAlternatingRowColors(True)
self.table_view.viewport().setMouseTracking(True)
self.table_view.setSortingEnabled(True)
self.table_view.setShowGrid(False)
self.table_view.verticalHeader().hide()
# self.table_view.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
self.unknown_model = UnknownGeneInfoModel()
self.unknown_view = QTableView()
self.unknown_view.setModel(self.unknown_model)
self.unknown_view.verticalHeader().hide()
self.unknown_view.setShowGrid(False)
self.unknown_view.setSelectionMode(QAbstractItemView.NoSelection)
self.unknown_view.horizontalHeader().setSectionResizeMode(
QHeaderView.Stretch)
self.splitter.addWidget(self.table_view)
self.splitter.addWidget(self.unknown_view)
self.splitter.setStretchFactor(0, 90)
self.splitter.setStretchFactor(1, 10)
self.mainArea.layout().addWidget(self.splitter)
def __init__(self):
super().__init__()
# ATTRIBUTES #
# input data
self.input_data = None
self.input_genes = None
self.tax_id = None
self.column_candidates = []
self.selected_gene_col = None
# input options
self.organisms = []
# gene matcher
self.gene_matcher = None
# threads
self.threadpool = QThreadPool(self)
self.workers = None
# progress bar
self.progress_bar = None
# filter
self.filter_labels = ['Unique', 'Partial', 'Unknown']
# GUI SECTION #
# Control area
self.info_box = widgetLabel(
widgetBox(self.controlArea, "Info", addSpace=True),
"Initializing\n")
organism_box = vBox(self.controlArea, 'Organism')
self.organism_select_combobox = comboBox(
organism_box,
self,
'selected_organism',
callback=self.on_input_option_change)
self.get_available_organisms()
self.organism_select_combobox.setCurrentIndex(self.selected_organism)
box = widgetBox(self.controlArea, 'Gene names')
self.gene_columns_model = itemmodels.DomainModel(
valid_types=(StringVariable, ))
self.gene_column_combobox = comboBox(
box,
self,
'selected_gene_col',
model=self.gene_columns_model,
sendSelectedValue=True,
callback=self.on_input_option_change)
self.attr_names_checkbox = checkBox(
box,
self,
'use_attr_names',
'Use attribute names',
disables=[(-1, self.gene_column_combobox)],
callback=self.on_input_option_change)
self.gene_column_combobox.setDisabled(bool(self.use_attr_names))
output_box = vBox(self.controlArea, 'Output settings')
# TODO: will widget support transposing tables?
# radioButtonsInBox(output_box, self, "gene_as_attr_name", ["Genes in rows", "Genes in columns"],
# callback=self.on_output_option_change)
# separator(output_box)
checkBox(output_box,
self,
'filter_unknown',
'Filter unknown genes',
callback=self.on_output_option_change)
separator(output_box)
output_box.layout().addWidget(horizontal_line())
checkBox(output_box,
self,
'include_entrez_id',
'Include Entrez ID',
callback=self.on_output_option_change)
# TODO: provide support for ensembl ids as output option
# checkBox(output_box, self, 'include_ensembl_id', 'Include Ensembl ID', callback=self.on_output_option_change)
auto_commit(self.controlArea, self, "auto_commit", label="Commit")
rubber(self.controlArea)
# Main area
filter_box = hBox(self.mainArea, 'Filter results')
self.radio_group = radioButtons(filter_box,
self,
value='selected_filter',
btnLabels=self.filter_labels,
orientation=Qt.Horizontal,
callback=self.on_filter_changed)
rubber(self.radio_group)
self.mainArea.layout().addWidget(filter_box)
self.proxy_model = FilterProxyModel(self)
self.extended_view = ExtendedTableView(parent=self)
self.extended_view.genes_view.setModel(self.proxy_model)
self.extended_view.genes_selection_model().selectionChanged.connect(
self.__selection_changed)
self.mainArea.layout().addWidget(self.extended_view, 1)
def __init__(self):
super().__init__()
self.res = None
self.orgnism = 352472
self.server = 'https://dictyexpress.research.bcm.edu'
self.headerLabels = [x[1] for x in Labels]
self.searchString = ""
self.items = []
self.lastSelected = None # store last selected customTreeItem
self.progress_bar = None
# threads
self.threadpool = QThreadPool()
# Login Section
box = gui.widgetBox(self.controlArea, 'Login')
self.namefield = gui.lineEdit(box,
self,
"username",
"Username:"******"password",
"Password:"******"setTimeVariable",
"Set Time variable")
self.time_var_checkBox.setToolTip(
'Create new column where each row represents one time point')
self.controlArea.layout().addWidget(h_line())
self.commit_button = gui.button(self.controlArea,
self,
"Commit",
callback=self.commit)
self.handle_commit_button(False)
self.refresh_button = gui.button(self.controlArea,
self,
"Refresh",
callback=self.refresh)
self.handle_cache_button(True)
gui.rubber(self.controlArea)
# Experiment Section
label = QLabel("Available projects:")
my_font = QFont()
my_font.setBold(True)
label.setFont(my_font)
self.mainArea.layout().addWidget(label)
self.mainArea.layout().addWidget(h_line())
self.filter = gui.lineEdit(self.mainArea,
self,
"searchString",
"Filter:",
callbackOnType=True,
callback=self.search_update)
self.experimentsWidget = QTreeWidget(alternatingRowColors=True,
rootIsDecorated=False,
uniformRowHeights=True,
sortingEnabled=True)
self.experimentsWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole))
self.experimentsWidget.selectionModel().selectionChanged.connect(
self.onSelectionChanged)
self.experimentsWidget.setHeaderLabels(self.headerLabels)
self.mainArea.layout().addWidget(self.experimentsWidget)
self.auth_set()
self.connect()
def __init__(self, parent=None):
super().__init__(parent)
# GUI
box = gui.widgetBox(self.controlArea, "Info", addSpace=True)
self.infoBox = gui.widgetLabel(box, "No data on input.")
box = gui.widgetBox(self.controlArea, "Split by", addSpace=True)
self.groupCombo = gui.comboBox(box,
self,
"selectedGroup",
callback=self.onGroupSelection)
gui.comboBox(self.controlArea,
self,
"selectedCenterMethod",
box="Center Fold-change Using",
items=[name for name, _ in self.CENTER_METHODS],
callback=self.onCenterMethodChange,
addSpace=True)
gui.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 = gui.doubleSpin(self.controlArea,
self,
"zCutoff",
0.0,
3.0,
0.01,
box="Z-Score Cutoff",
callback=[self.replotMA, self.commitIf])
gui.separator(self.controlArea)
box = gui.widgetBox(self.controlArea, "Ouput")
gui.checkBox(box,
self,
"appendZScore",
"Append Z-Scores",
tooltip="Append calculated Z-Scores to output",
callback=self.commitIf)
gui.checkBox(box,
self,
"appendRIValues",
"Append Log Ratio and Intensity values",
tooltip="Append calculated Log Ratio and Intensity "
"values to output data",
callback=self.commitIf)
gui.rubber(self.controlArea)
gui.auto_commit(self.controlArea, self, "autoCommit", "Commit")
self.graph = pg.PlotWidget(background="w")
self.graph.getAxis("bottom").setLabel(
"Intensity: log<sub>10</sub>(R*G)")
self.graph.getAxis("left").setLabel("Log ratio: log<sub>2</sub>(R/G)")
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._executor = concurrent.ThreadExecutor(threadPool=QThreadPool(
maxThreadCount=1))