def __init__(self, parent=None, *, show_navbar=True):
super().__init__(parent)
mpl.rcParams.update({
"text.color": "white",
"axes.labelcolor": "white",
"xtick.color": "white",
"ytick.color": "white",
"font.size": 8
})
layout = QVBoxLayout(self)
layout.setContentsMargins(0, 0, 0, 0)
self.figure = Figure(facecolor="none")
self.canvas = WrappedCanvas(self.figure)
self.setStyleSheet("background-color:palette(alternate-base);")
layout.addWidget(self.canvas)
if not show_navbar:
return
navbar = NavBar(self.canvas, self, coordinates=False)
navbar_container = QWidget()
navbar_container.setContentsMargins(0, 0, 0, 0)
navbar_container.setFixedHeight(50)
navbar_layout = QHBoxLayout(navbar_container)
navbar_layout.addWidget(navbar)
navbar_layout.setAlignment(navbar, Qt.AlignCenter)
layout.addWidget(navbar_container)
def __init__(self, parent=None):
super().__init__(parent=parent)
setMplDefaults()
self.plot = MPLPlot()
layout = QtGui.QVBoxLayout(self)
layout.addWidget(self.plot)
layout.addWidget(NavBar(self.plot, self))
def initUI(self):
# The graph widgets
self.Graph = PlotCanvas(False, False, parent=self)
self.toolbar = NavBar(self.Graph, self)
control_panel = ButtonPanel(self)
fncs.AllInOneLayout(self, [self.Graph, control_panel],
Stretches=[4, 1],
VH='h')
self.show()
def __init__(self, parent=None):
super().__init__(parent=parent)
setMplDefaults()
self.plot = MPLPlot()
self.mplBar = NavBar(self.plot, self)
self.addMplBarOptions()
self.mplBar.setIconSize(QtCore.QSize(16, 16))
self.layout = QtGui.QVBoxLayout(self)
self.layout.addWidget(self.plot)
self.layout.addWidget(self.mplBar)
def __init__(self, parent=None):
super().__init__(parent=parent)
setMplDefaults()
self.plot = MPLPlot()
self.mplBar = NavBar(self.plot, self)
self.addMplBarOptions()
self.toolLayout = QtGui.QHBoxLayout()
self.layout = QtGui.QVBoxLayout(self)
self.layout.addLayout(self.toolLayout)
self.layout.addWidget(self.plot)
self.layout.addWidget(self.mplBar)
def __init__(self, parent: Optional[QtWidgets.QWidget] = None):
super().__init__(parent=parent)
#: the plot widget
self.plot = MPLPlot()
#: the matplotlib toolbar
self.mplBar = NavBar(self.plot, self)
self.addMplBarOptions()
defaultIconSize = int(16 * dpiScalingFactor(self))
self.mplBar.setIconSize(QtCore.QSize(defaultIconSize, defaultIconSize))
layout = QtWidgets.QVBoxLayout(self)
layout.addWidget(self.plot)
layout.addWidget(self.mplBar)
self.setLayout(layout)
def __init__(self, parent, log_handlers: [StreamHandler]):
self._logger = getLogger(__name__)
for h in log_handlers:
self._logger.addHandler(h)
self._logger.debug("Initializing")
super().__init__(Figure(figsize=(5, 5)))
self.setParent(parent)
self._new = True
self._nav_bar = NavBar(self, parent)
self._nav_bar.update()
# self._leg_plot_links = dict()
self._plots = list() # name, coords, active
self._v_lines = list()
self._base_strings = dict()
# self.figure.canvas.mpl_connect('pick_event', self._onpick)
self._logger.debug("Initialized")
def __init__(self, parent: Optional[QtWidgets.QWidget] = None):
super().__init__(parent=parent)
setMplDefaults(self)
scaling = np.rint(self.logicalDpiX() / 96.0)
defaultIconSize = 16 * scaling
self.plot = MPLPlot()
self.mplBar = NavBar(self.plot, self)
self.addMplBarOptions()
self.mplBar.setIconSize(QtCore.QSize(defaultIconSize, defaultIconSize))
layout = QtWidgets.QVBoxLayout(self)
layout.addWidget(self.plot)
layout.addWidget(self.mplBar)
self.setLayout(layout)
def __init__(self, data_id, parent=None):
super().__init__(parent)
self.data_id = data_id
search_str = 'run ID = '
idx = self.data_id.find(search_str) + len(search_str)
run_id = int(self.data_id[idx:].strip())
self.setWindowTitle(f"{get_app_title()} (#{run_id})")
self.active_dataset = None
self.data = {}
self.data_struct = {}
self.adding_queue = {}
self.plot_data_pending = False
self.current_plot_choice_info = None
# plot settings
set_matplotlib_defaults()
# data chosing widgets
self.structure_widget = DataStructure()
self.plot_choice = PlotChoice()
chooser_layout = QtWidgets.QVBoxLayout()
chooser_layout.addWidget(self.structure_widget)
chooser_layout.addWidget(self.plot_choice)
# plot control widgets
self.plot = MPLPlot(width=5, height=4)
plot_layout = QtWidgets.QVBoxLayout()
plot_layout.addWidget(self.plot)
plot_layout.addWidget(NavBar(self.plot, self))
# Main layout
self.frame = QtWidgets.QFrame()
main_layout = QtWidgets.QHBoxLayout(self.frame)
main_layout.addLayout(chooser_layout)
main_layout.addLayout(plot_layout)
# data processing threads
self.data_adder = DataAdder()
self.data_adder_thread = QtCore.QThread()
self.data_adder.moveToThread(self.data_adder_thread)
self.data_adder.data_updated.connect(self.data_from_adder)
self.data_adder.data_updated.connect(self.data_adder_thread.quit)
self.data_adder_thread.started.connect(self.data_adder.run)
self.plot_data = PlotData()
self.plot_data_thread = QtCore.QThread()
self.plot_data.moveToThread(self.plot_data_thread)
self.plot_data.data_processed.connect(self.update_plot)
self.plot_data.data_processed.connect(self.plot_data_thread.quit)
self.plot_data_thread.started.connect(self.plot_data.process_data)
# signals/slots for data selection etc.
self.data_added.connect(self.structure_widget.update)
self.data_added.connect(self.update_plot_data)
self.structure_widget.itemSelectionChanged.connect(self.activate_data)
self.data_activated.connect(self.plot_choice.set_options)
self.plot_choice.choice_updated.connect(self.update_plot_data)
# activate window
self.frame.setFocus()
self.setCentralWidget(self.frame)
self.activateWindow()
def __init__(self) -> None:
"""ViolinGUI Constructor. Defines all aspects of the GUI."""
# ## Setup section
# Inherits from QMainWindow
super().__init__()
self.rootdir = get_project_root()
# QMainWindow basic properties
self.setWindowTitle("SCOUTS - Violins")
self.setWindowIcon(
QIcon(
os.path.abspath(os.path.join(self.rootdir, 'src',
'scouts.ico'))))
# Creates QWidget as QMainWindow's central widget
self.page = QWidget(self)
self.setCentralWidget(self.page)
# Miscellaneous initialization values
self.threadpool = QThreadPool() # Threadpool for workers
self.population_df = None # DataFrame of whole population (raw data)
self.summary_df = None # DataFrame indicating which SCOUTS output corresponds to which rule
self.summary_path = None # path to all DataFrames generated by SCOUTS
self.main_layout = QVBoxLayout(self.page)
# Title section
# Title
self.title = QLabel(self.page)
self.title.setText('SCOUTS - Violins')
self.title.setStyleSheet(self.style['title'])
self.title.adjustSize()
self.main_layout.addWidget(self.title)
# ## Input section
# Input header
self.input_header = QLabel(self.page)
self.input_header.setText('Load data')
self.input_header.setStyleSheet(self.style['header'])
self.input_header.adjustSize()
self.main_layout.addWidget(self.input_header)
# Input/Output frame
self.input_frame = QFrame(self.page)
self.input_frame.setFrameShape(QFrame.StyledPanel)
self.input_frame.setLayout(QFormLayout())
self.main_layout.addWidget(self.input_frame)
# Raw data button
self.input_button = QPushButton(self.page)
self.input_button.setStyleSheet(self.style['button'])
self.set_icon(self.input_button, 'x-office-spreadsheet')
self.input_button.setObjectName('file')
self.input_button.setText(' Load raw data file')
self.input_button.setToolTip(
'Load raw data file (the file given to SCOUTS as the input file)')
self.input_button.clicked.connect(self.get_path)
# SCOUTS results button
self.output_button = QPushButton(self.page)
self.output_button.setStyleSheet(self.style['button'])
self.set_icon(self.output_button, 'folder')
self.output_button.setObjectName('folder')
self.output_button.setText(' Load SCOUTS results')
self.output_button.setToolTip(
'Load data from SCOUTS analysis '
'(the folder given to SCOUTS as the output folder)')
self.output_button.clicked.connect(self.get_path)
# Add widgets above to input frame Layout
self.input_frame.layout().addRow(self.input_button)
self.input_frame.layout().addRow(self.output_button)
# ## Samples section
# Samples header
self.samples_header = QLabel(self.page)
self.samples_header.setText('Select sample names')
self.samples_header.setStyleSheet(self.style['header'])
self.samples_header.adjustSize()
self.main_layout.addWidget(self.samples_header)
# Samples frame
self.samples_frame = QFrame(self.page)
self.samples_frame.setFrameShape(QFrame.StyledPanel)
self.samples_frame.setLayout(QFormLayout())
self.main_layout.addWidget(self.samples_frame)
# Samples label
self.samples_label = QLabel(self.page)
self.samples_label.setText(
'Write sample names delimited by semicolons below.\nEx: Control;Treat_01;Pac-03'
)
self.samples_label.setStyleSheet(self.style['label'])
# Sample names line edit
self.sample_names = QLineEdit(self.page)
self.sample_names.setStyleSheet(self.style['line edit'])
# Add widgets above to samples frame Layout
self.samples_frame.layout().addRow(self.samples_label)
self.samples_frame.layout().addRow(self.sample_names)
# ## Analysis section
# Analysis header
self.analysis_header = QLabel(self.page)
self.analysis_header.setText('Plot parameters')
self.analysis_header.setStyleSheet(self.style['header'])
self.analysis_header.adjustSize()
self.main_layout.addWidget(self.analysis_header)
# Analysis frame
self.analysis_frame = QFrame(self.page)
self.analysis_frame.setFrameShape(QFrame.StyledPanel)
self.analysis_frame.setLayout(QFormLayout())
self.main_layout.addWidget(self.analysis_frame)
# Analysis labels
self.analysis_label_01 = QLabel(self.page)
self.analysis_label_01.setText('Compare')
self.analysis_label_01.setStyleSheet(self.style['label'])
self.analysis_label_02 = QLabel(self.page)
self.analysis_label_02.setText('with')
self.analysis_label_02.setStyleSheet(self.style['label'])
self.analysis_label_03 = QLabel(self.page)
self.analysis_label_03.setText('for marker')
self.analysis_label_03.setStyleSheet(self.style['label'])
self.analysis_label_04 = QLabel(self.page)
self.analysis_label_04.setText('Outlier type')
self.analysis_label_04.setStyleSheet(self.style['label'])
# Analysis drop-down boxes
self.drop_down_01 = QComboBox(self.page)
self.drop_down_01.addItems([
'whole population', 'non-outliers', 'top outliers',
'bottom outliers', 'none'
])
self.drop_down_01.setStyleSheet(self.style['drop down'])
self.drop_down_01.setCurrentIndex(2)
self.drop_down_02 = QComboBox(self.page)
self.drop_down_02.addItems([
'whole population', 'non-outliers', 'top outliers',
'bottom outliers', 'none'
])
self.drop_down_02.setStyleSheet(self.style['drop down'])
self.drop_down_02.setCurrentIndex(0)
self.drop_down_03 = QComboBox(self.page)
self.drop_down_03.setStyleSheet(self.style['drop down'])
self.drop_down_04 = QComboBox(self.page)
self.drop_down_04.addItems(['OutS', 'OutR'])
self.drop_down_04.setStyleSheet(self.style['drop down'])
# Add widgets above to samples frame Layout
self.analysis_frame.layout().addRow(self.analysis_label_01,
self.drop_down_01)
self.analysis_frame.layout().addRow(self.analysis_label_02,
self.drop_down_02)
self.analysis_frame.layout().addRow(self.analysis_label_03,
self.drop_down_03)
self.analysis_frame.layout().addRow(self.analysis_label_04,
self.drop_down_04)
self.legend_checkbox = QCheckBox(self.page)
self.legend_checkbox.setText('Add legend to the plot')
self.legend_checkbox.setStyleSheet(self.style['checkbox'])
self.main_layout.addWidget(self.legend_checkbox)
# Plot button (stand-alone)
self.plot_button = QPushButton(self.page)
self.set_icon(self.plot_button, 'system-run')
self.plot_button.setText(' Plot')
self.plot_button.setToolTip(
'Plot data after loading the input data and selecting parameters')
self.plot_button.setStyleSheet(self.style['run button'])
self.plot_button.setEnabled(False)
self.plot_button.clicked.connect(self.run_plot)
self.main_layout.addWidget(self.plot_button)
# ## Secondary Window
# This is used to plot the violins only
self.secondary_window = QMainWindow(self)
self.secondary_window.resize(720, 720)
self.dynamic_canvas = DynamicCanvas(self.secondary_window,
width=6,
height=6,
dpi=120)
self.secondary_window.setCentralWidget(self.dynamic_canvas)
self.secondary_window.addToolBar(
NavBar(self.dynamic_canvas, self.secondary_window))
def __init__(self, dataId, parent=None):
super().__init__(parent)
self.dataId = dataId
self.setWindowTitle(getAppTitle() + f" ({dataId})")
self.data = {}
self.addingQueue = {}
self.currentlyProcessingPlotData = False
self.pendingPlotData = False
# plot settings
setMplDefaults()
# data chosing widgets
self.structureWidget = DataStructure()
self.plotChoice = PlotChoice()
chooserLayout = QVBoxLayout()
chooserLayout.addWidget(self.structureWidget)
chooserLayout.addWidget(self.plotChoice)
# plot control widgets
self.plot = MPLPlot()
plotLayout = QVBoxLayout()
plotLayout.addWidget(self.plot)
plotLayout.addWidget(NavBar(self.plot, self))
# Main layout
self.frame = QFrame()
mainLayout = QHBoxLayout(self.frame)
mainLayout.addLayout(chooserLayout)
mainLayout.addLayout(plotLayout)
# data processing threads
self.dataAdder = DataAdder()
self.dataAdderThread = QThread()
self.dataAdder.moveToThread(self.dataAdderThread)
self.dataAdder.dataUpdated.connect(self.dataFromAdder)
self.dataAdder.dataUpdated.connect(self.dataAdderThread.quit)
self.dataAdderThread.started.connect(self.dataAdder.run)
self.plotData = PlotData()
self.plotDataThread = QThread()
self.plotData.moveToThread(self.plotDataThread)
self.plotData.dataProcessed.connect(self.updatePlot)
self.plotData.dataProcessed.connect(self.plotDataThread.quit)
self.plotDataThread.started.connect(self.plotData.processData)
# signals/slots for data selection etc.
self.dataAdded.connect(self.structureWidget.update)
self.dataAdded.connect(self.updatePlotChoices)
self.dataAdded.connect(self.updatePlotData)
self.structureWidget.itemSelectionChanged.connect(self.activateData)
self.dataActivated.connect(self.plotChoice.setOptions)
self.plotChoice.choiceUpdated.connect(self.updatePlotData)
# activate window
self.frame.setFocus()
self.setCentralWidget(self.frame)
self.activateWindow()
def __init__(self, parent):
self.figure = plt.figure(facecolor='white')
self.canvas = Canvas(self.figure)
self.toolbar = NavBar(self.canvas, parent)