class AddActionText(UsesQApplication):
'''Test case for calling QToolbar.addAction passing a text'''
def setUp(self):
#Acquire resources
super(AddActionText, self).setUp()
self.window = QMainWindow()
self.toolbar = QToolBar()
self.window.addToolBar(self.toolbar)
def tearDown(self):
#Release resources
super(AddActionText, self).tearDown()
del self.toolbar
del self.window
def testText(self):
#QToolBar.addAction(text) - add a QToolButton
self.toolbar.addAction('aaaa')
self.assertEqual(len(self.toolbar.actions()), 1)
action = self.toolbar.actions()[0]
self.assert_(isinstance(action, QAction))
self.assertEqual(action.text(), 'aaaa')
class AddActionText(UsesQApplication):
'''Test case for calling QToolbar.addAction passing a text'''
def setUp(self):
#Acquire resources
super(AddActionText, self).setUp()
self.window = QMainWindow()
self.toolbar = QToolBar()
self.window.addToolBar(self.toolbar)
def tearDown(self):
#Release resources
super(AddActionText, self).tearDown()
del self.toolbar
del self.window
def testText(self):
#QToolBar.addAction(text) - add a QToolButton
self.toolbar.addAction('aaaa')
self.assertEqual(len(self.toolbar.actions()), 1)
action = self.toolbar.actions()[0]
self.assert_(isinstance(action, QAction))
self.assertEqual(action.text(), 'aaaa')
else:
lbl.setText('')
sim.cleanup()
t.stop()
benc_timer.stop()
action.changed.connect(_handle_sim_action)
toolbar = QToolBar()
lbl = QLabel()
benc_timer = QTimer(w)
def _on_bench():
global ticks
lbl.setText(f'Frequency: {ticks} Hz')
ticks = 0
benc_timer.timeout.connect(_on_bench)
toolbar.addAction(action)
toolbar.addSeparator()
toolbar.addWidget(lbl)
w.addToolBar(toolbar)
w.setCentralWidget(ed)
w.setWindowTitle(make_title())
w.show()
app.exec_()
class ViolinGUI(QMainWindow):
"""Main Window Widget for ViolinGUI."""
style = {
'title': 'QLabel {font-size: 18pt; font-weight: 600}',
'header': 'QLabel {font-size: 12pt; font-weight: 520}',
'label': 'QLabel {font-size: 10pt}',
'button': 'QPushButton {font-size: 10pt}',
'run button': 'QPushButton {font-size: 18pt; font-weight: 600}',
'line edit': 'QLineEdit {font-size: 10pt}',
'checkbox': 'QCheckBox {font-size: 10pt}',
'drop down': 'QComboBox {font-size: 10pt}'
}
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 set_icon(self, widget: QWidget, icon: str) -> None:
"""Associates an icon to a widget."""
i = QIcon()
i.addPixmap(
QPixmap(
os.path.abspath(
os.path.join(self.rootdir, 'src', 'default_icons',
f'{icon}.svg'))))
widget.setIcon(QIcon.fromTheme(icon, i))
def get_path(self) -> None:
"""Opens a dialog box and loads the corresponding data into memory, depending on the caller widget."""
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
query = None
func = None
if self.sender().objectName() == 'file':
query, _ = QFileDialog.getOpenFileName(self,
"Select file",
"",
"All Files (*)",
options=options)
func = self.load_scouts_input_data
elif self.sender().objectName() == 'folder':
query = QFileDialog.getExistingDirectory(self,
"Select Directory",
options=options)
func = self.load_scouts_results
if query:
self.load_data(query, func)
def load_data(self, query: str, func: Callable) -> None:
"""Loads input data into memory, while displaying a loading message as a separate worker."""
worker = Worker(func=func, query=query)
message = self.loading_message()
worker.signals.started.connect(message.show)
worker.signals.started.connect(self.page.setDisabled)
worker.signals.error.connect(self.generic_error_message)
worker.signals.error.connect(message.destroy)
worker.signals.failed.connect(self.plot_button.setDisabled)
worker.signals.success.connect(message.destroy)
worker.signals.success.connect(self.enable_plot)
worker.signals.finished.connect(self.page.setEnabled)
self.threadpool.start(worker)
def loading_message(self) -> QDialog:
"""Returns the message box to be displayed while the user waits for the input data to load."""
message = QDialog(self)
message.setWindowTitle('Loading')
message.resize(300, 50)
label = QLabel('loading DataFrame into memory...', message)
label.setStyleSheet(self.style['label'])
label.adjustSize()
label.setAlignment(Qt.AlignCenter)
label.move(int((message.width() - label.width()) / 2),
int((message.height() - label.height()) / 2))
return message
def load_scouts_input_data(self, query: str) -> None:
"""Loads data for whole population prior to SCOUTS into memory (used for plotting the whole population)."""
try:
self.population_df = pd.read_excel(query, index_col=0)
except XLRDError:
self.population_df = pd.read_csv(query, index_col=0)
self.drop_down_03.clear()
self.drop_down_03.addItems(list(self.population_df.columns))
self.drop_down_03.setCurrentIndex(0)
def load_scouts_results(self, query: str) -> None:
"""Loads the SCOUTS summary file into memory, in order to dynamically locate SCOUTS output files later when
the user chooses which data to plot."""
self.summary_df = pd.read_excel(os.path.join(query, 'summary.xlsx'),
index_col=None)
self.summary_path = query
def enable_plot(self) -> None:
"""Enables plot button if all necessary files are placed in memory."""
if isinstance(self.summary_df, pd.DataFrame) and isinstance(
self.population_df, pd.DataFrame):
self.plot_button.setEnabled(True)
def run_plot(self) -> None:
"""Sets and starts the plot worker."""
worker = Worker(func=self.plot)
worker.signals.error.connect(self.generic_error_message)
worker.signals.success.connect(self.secondary_window.show)
self.threadpool.start(worker)
def plot(self) -> None:
"""Logic for plotting data based on user selection of populations, markers, etc."""
# Clear figure currently on plot
self.dynamic_canvas.axes.cla()
# Initialize values and get parameters from GUI
columns = ['sample', 'marker', 'population', 'expression']
samples = self.parse_sample_names()
pop_01 = self.drop_down_01.currentText()
pop_02 = self.drop_down_02.currentText()
pops_to_analyse = [pop_01, pop_02]
marker = self.drop_down_03.currentText()
cutoff_from_reference = True if self.drop_down_04.currentText(
) == 'OutR' else False
violin_df = pd.DataFrame(columns=columns)
# Start fetching data from files
# Whole population
for pop in pops_to_analyse:
if pop == 'whole population':
for partial_df in self.yield_violin_values(
df=self.population_df,
population='whole population',
samples=samples,
marker=marker,
columns=columns):
violin_df = violin_df.append(partial_df)
# Other comparisons
elif pop != 'none':
for file_number in self.yield_selected_file_numbers(
summary_df=self.summary_df,
population=pop,
cutoff_from_reference=cutoff_from_reference,
marker=marker):
df_path = os.path.join(self.summary_path, 'data',
f'{"%04d" % file_number}.')
try:
sample_df = pd.read_excel(df_path + 'xlsx',
index_col=0)
except FileNotFoundError:
sample_df = pd.read_csv(df_path + 'csv', index_col=0)
if not sample_df.empty:
for partial_df in self.yield_violin_values(
df=sample_df,
population=pop,
samples=samples,
marker=marker,
columns=columns):
violin_df = violin_df.append(partial_df)
# Plot data
pops_to_analyse = [p for p in pops_to_analyse if p != 'none']
violin_df = violin_df[violin_df['marker'] == marker]
for pop in pops_to_analyse:
pop_subset = violin_df.loc[violin_df['population'] == pop]
for sample in samples:
sample_subset = pop_subset.loc[pop_subset['sample'] == sample]
sat = 1.0 - samples.index(sample) / (len(samples) + 1)
self.dynamic_canvas.update_figure(
subset_by_sample=sample_subset,
pop=pop,
sat=sat,
samples=samples)
# Draw plotted data on canvas
if self.legend_checkbox.isChecked():
self.dynamic_canvas.add_legend()
self.dynamic_canvas.axes.set_title(
f'{marker} expression - {self.drop_down_04.currentText()}')
self.dynamic_canvas.fig.canvas.draw()
def parse_sample_names(self) -> List[str]:
"""Parse sample names from the QLineEdit Widget."""
return self.sample_names.text().split(';')
def generic_error_message(self, error: Tuple[Exception, str]) -> None:
"""Error message box used to display any error message (including traceback) for any uncaught errors."""
name, trace = error
QMessageBox.critical(
self, 'An error occurred!',
f"Error: {str(name)}\n\nfull traceback:\n{trace}")
def closeEvent(self, event: QEvent) -> None:
"""Defines the message box for when the user wants to quit ViolinGUI."""
title = 'Quit Application'
mes = "Are you sure you want to quit?"
reply = QMessageBox.question(self, title, mes,
QMessageBox.Yes | QMessageBox.No,
QMessageBox.No)
if reply == QMessageBox.Yes:
self.setEnabled(False)
self.threadpool.waitForDone()
event.accept()
else:
event.ignore()
@staticmethod
def yield_violin_values(df: pd.DataFrame, population: str,
samples: List[str], marker: str,
columns: List[str]) -> pd.DataFrame:
"""Returns a DataFrame from expression values, along with information of sample, marker and population. This
DataFrame is appended to the violin plot DataFrame in order to simplify plotting the violins afterwards."""
for sample in samples:
series = df.loc[df.index.str.contains(sample)].loc[:, marker]
yield pd.DataFrame(
{
'sample': sample,
'marker': marker,
'population': population,
'expression': series
},
columns=columns)
@staticmethod
def yield_selected_file_numbers(
summary_df: pd.DataFrame, population: str,
cutoff_from_reference: bool,
marker: str) -> Generator[pd.DataFrame, None, None]:
"""Yields file numbers from DataFrames resulting from SCOUTS analysis. DataFrames are yielded based on
global values, i.e. the comparisons the user wants to perform."""
cutoff = 'sample'
if cutoff_from_reference is True:
cutoff = 'reference'
for index, (file_number, cutoff_from, reference, outliers_for,
category) in summary_df.iterrows():
if cutoff_from == cutoff and outliers_for == marker and category == population:
yield file_number
tool_bar.addAction(open_dir_action)
open_file_action = QAction(
QIcon(QCommonStyle().standardPixmap(QCommonStyle.SP_FileIcon)), '新建文件')
tool_bar.addAction(open_file_action)
open_delete_action = QAction(
QIcon(QCommonStyle().standardPixmap(QCommonStyle.SP_TrashIcon)), '删除')
tool_bar.addAction(open_delete_action)
dock_calendar_widget = QDockWidget()
dock_calendar_widget.setWidget(QCalendarWidget())
dock_listview_widget = QDockWidget()
dock_listview_widget.setWidget(QListView())
# 添加在dock widgets区域的右边，Qt是一个包含了各种常量的包
mainwindow.addDockWidget(Qt.RightDockWidgetArea, dock_calendar_widget)
mainwindow.addDockWidget(Qt.RightDockWidgetArea, dock_listview_widget)
# 添加一个空的widget
mainwindow.setCentralWidget(QWidget())
# 创建状态栏对象
statusbar = QStatusBar()
statusbar.showMessage('我是statusbar')
# 添加工具栏
mainwindow.addToolBar(tool_bar)
# 添加状态栏
mainwindow.setStatusBar(statusbar)
mainwindow.show()
app.exec_()
