def __init__(self):
super().__init__()
info_box = gui.widgetBox(self.controlArea, "Info")
self.info_label = QLabel()
info_box.layout().addWidget(self.info_label)
self.res = ResolweHelper()
data_objects = self.res.list_data_objects(self.DATA_TYPE)
descriptor_schema = self.res.get_descriptor_schema(
self.DESCRIPTOR_SCHEMA)
self.res_widget = ResolweDataWidget(data_objects, descriptor_schema)
self.res_widget.view.selectionModel().selectionChanged.connect(
self.commit)
self.res_widget.set_target_column(self.res_widget.header.target)
self.__assign_delegates()
self.udpdate_info_box()
self.mainArea.layout().addWidget(self.res_widget)
self.controlArea.layout().addStretch(10)
gui.auto_commit(self.controlArea, self, "auto_commit", "&Commit")
print(os.environ.get('RESOLWE_HOST_URL'))
print(os.environ.get('RESOLWE_API_USERNAME'))
print(os.environ.get('RESOLWE_API_PASSWORD'))
def main(args=None):
if args is None:
args = sys.argv
app = QApplication(list(args))
w = OWResolweDataObject()
res = ResolweHelper()
w.set_data(res.get_object(id=197))
# w.resetSettings()
w.show()
w.raise_()
rv = app.exec_()
w.saveSettings()
w.onDeleteWidget()
return rv
def __init__(self):
super().__init__()
self.data_table_object = None # type: Optional[resolwe.Data]
# threading
self._task = None # type: Optional[ResolweTask]
self._executor = ThreadExecutor()
box = gui.widgetBox(self.controlArea, 'Data Object')
self._data_obj = QLabel(box)
box.layout().addWidget(self._data_obj)
box = gui.widgetBox(self.controlArea, 'Process info')
self._proc_info = QLabel(box)
box.layout().addWidget(self._proc_info)
box = gui.widgetBox(self.controlArea, 'User permissions')
self._usr_perm = QLabel(box)
box.layout().addWidget(self._usr_perm)
self.controlArea.setMinimumWidth(self.controlArea.sizeHint().width())
self.layout().setSizeConstraint(QLayout.SetFixedSize)
gui.auto_commit(self.controlArea, self, "auto_commit", "Download data")
self.res = ResolweHelper()
class OWResolwetSNE(OWWidget):
name = "t-SNE"
description = "Two-dimensional data projection with t-SNE."
icon = "icons/OWResolwetSNE.svg"
priority = 50
class Inputs:
data = Input("Data", resolwe.Data, default=True)
class Outputs:
selected_data = Output("Selected Data", resolwe.Data, default=True)
settings_version = 2
#: Runtime state
Running, Finished, Waiting = 1, 2, 3
settingsHandler = settings.DomainContextHandler()
max_iter = settings.Setting(300)
perplexity = settings.Setting(30)
pca_components = settings.Setting(20)
# output embedding role.
NoRole, AttrRole, AddAttrRole, MetaRole = 0, 1, 2, 3
auto_commit = settings.Setting(True)
selection_indices = settings.Setting(None, schema_only=True)
legend_anchor = settings.Setting(((1, 0), (1, 0)))
graph = SettingProvider(OWMDSGraph)
jitter_sizes = [0, 0.1, 0.5, 1, 2, 3, 4, 5, 7, 10]
graph_name = "graph.plot_widget.plotItem"
class Error(OWWidget.Error):
not_enough_rows = Msg("Input data needs at least 2 rows")
constant_data = Msg("Input data is constant")
no_attributes = Msg("Data has no attributes")
out_of_memory = Msg("Out of memory")
optimization_error = Msg("Error during optimization\n{}")
def __init__(self):
super().__init__()
#: Effective data used for plot styling/annotations.
self.data = None # type: Optional[Orange.data.Table]
#: Input subset data table
self.subset_data = None # type: Optional[Orange.data.Table]
#: Input data table
self.signal_data = None
# resolwe variables
self.data_table_object = None # type: Optional[resolwe.Data]
self._tsne_slug = 't-sne'
self._tsne_selection_slug = 't-sne-selection'
self._embedding_data_object = None
self._embedding = None
self._embedding_clas_var = None
self.variable_x = ContinuousVariable("tsne-x")
self.variable_y = ContinuousVariable("tsne-y")
# threading
self._task = None # type: Optional[ResolweTask]
self._executor = ThreadExecutor()
self.res = ResolweHelper()
self._subset_mask = None # type: Optional[np.ndarray]
self._invalidated = False
self.pca_data = None
self._curve = None
self._data_metas = None
self.variable_x = ContinuousVariable("tsne-x")
self.variable_y = ContinuousVariable("tsne-y")
self.__update_loop = None
self.__in_next_step = False
self.__draw_similar_pairs = False
box = gui.vBox(self.controlArea, "t-SNE")
form = QFormLayout(labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow,
verticalSpacing=10)
form.addRow("Max iterations:",
gui.spin(box, self, "max_iter", 250, 2000, step=50))
form.addRow("Perplexity:",
gui.spin(box, self, "perplexity", 1, 100, step=1))
box.layout().addLayout(form)
gui.separator(box, 10)
self.runbutton = gui.button(box,
self,
"Run",
callback=self._run_embeding)
box = gui.vBox(self.controlArea, "PCA Preprocessing")
gui.hSlider(box,
self,
'pca_components',
label="Components: ",
minValue=2,
maxValue=50,
step=1) #, callback=self._initialize)
box = gui.vBox(self.mainArea, True, margin=0)
self.graph = OWMDSGraph(self,
box,
"MDSGraph",
view_box=MDSInteractiveViewBox)
box.layout().addWidget(self.graph.plot_widget)
self.plot = self.graph.plot_widget
g = self.graph.gui
box = g.point_properties_box(self.controlArea)
self.models = g.points_models
# Because sc data frequently has many genes,
# showing all attributes in combo boxes can cause problems
# QUICKFIX: Remove a separator and attributes from order
# (leaving just the class and metas)
for model in self.models:
model.order = model.order[:-2]
g.add_widgets(ids=[g.JitterSizeSlider], widget=box)
box = gui.vBox(self.controlArea, "Plot Properties")
g.add_widgets([
g.ShowLegend, g.ToolTipShowsAll, g.ClassDensity,
g.LabelOnlySelected
], box)
self.controlArea.layout().addStretch(100)
self.icons = gui.attributeIconDict
palette = self.graph.plot_widget.palette()
self.graph.set_palette(palette)
gui.rubber(self.controlArea)
self.graph.box_zoom_select(self.controlArea)
gui.auto_commit(self.controlArea, self, "auto_commit",
"Send Selection", "Send Automatically")
self.plot.getPlotItem().hideButtons()
self.plot.setRenderHint(QPainter.Antialiasing)
self.graph.jitter_continuous = True
# self._initialize()
def update_colors(self):
pass
def update_density(self):
self.update_graph(reset_view=False)
def update_regression_line(self):
self.update_graph(reset_view=False)
def prepare_data(self):
pass
def update_graph(self, reset_view=True, **_):
self.graph.zoomStack = []
if self.graph.data is None:
return
self.graph.update_data(self.variable_x,
self.variable_y,
reset_view=True)
def reset_graph_data(self, *_):
if self.data is not None:
self.graph.rescale_data()
self.update_graph()
def selection_changed(self):
if self._task:
self.cancel(clear_state=False)
self._task = None
self._executor = ThreadExecutor()
self.commit()
def _clear_plot(self):
self.graph.plot_widget.clear()
def _clear_state(self):
self._clear_plot()
self.graph.new_data(None)
self._embedding_data_object = None
self._embedding = None
self._embedding_clas_var = None
self._task = None
self._executor = ThreadExecutor()
def cancel(self, clear_state=True):
"""Cancel the current task (if any)."""
if self._task is not None:
self._executor.shutdown(wait=False)
self.runbutton.setText('Run')
self.progressBarFinished()
if clear_state:
self._clear_state()
def run_task(self, slug, func):
if self._task is not None:
try:
self.cancel()
except CancelledError as e:
print(e)
assert self._task is None
self.progressBarInit()
self._task = ResolweTask(slug)
self._task.future = self._executor.submit(func)
self._task.watcher = FutureWatcher(self._task.future)
self._task.watcher.finished.connect(self.task_finished)
@Slot(Future, name='Finished')
def task_finished(self, future):
assert threading.current_thread() == threading.main_thread()
assert self._task is not None
assert self._task.future is future
assert future.done()
try:
future_result = future.result()
except Exception as ex:
# TODO: raise exceptions
raise ex
else:
if self._task.slug == self._tsne_slug:
self._embedding_data_object = future_result
self._embedding_clas_var = self.res.get_json(
self._embedding_data_object, 'class_var')
self._embedding = np.array(
self.res.get_json(self._embedding_data_object,
'embedding_json', 'embedding'))
self._setup_plot()
if self._task.slug == self._tsne_selection_slug:
print(future_result)
self.Outputs.selected_data.send(future_result)
finally:
self.progressBarFinished()
self.runbutton.setText('Start')
self._task = None
@Inputs.data
def set_data(self, data):
# type: (Optional[resolwe.Data]) -> None
if data:
self.data_table_object = data
self._run_embeding()
def _run_embeding(self):
if self._task:
self.cancel()
return
if self._task is None:
inputs = {
'data_table': self.data_table_object,
'pca_components': self.pca_components,
'perplexity': self.perplexity,
'iterations': self.max_iter
}
if self._embedding is not None and self._embedding_data_object is not None:
inputs['init'] = self._embedding_data_object
func = partial(self.res.run_process, self._tsne_slug, **inputs)
# move filter process in thread
self.run_task(self._tsne_slug, func)
self.runbutton.setText('Stop')
def _setup_plot(self):
class_var = DiscreteVariable(self._embedding_clas_var['name'],
values=self._embedding_clas_var['values'])
y_data = self._embedding_clas_var['y_data']
data = np.c_[self._embedding, y_data]
plot_data = Table(
Domain([self.variable_x, self.variable_y], class_vars=class_var),
data)
domain = plot_data and len(plot_data) and plot_data.domain or None
for model in self.models:
model.set_domain(domain)
self.graph.attr_color = plot_data.domain.class_var if domain else None
self.graph.attr_shape = None
self.graph.attr_size = None
self.graph.attr_label = None
self.graph.new_data(plot_data)
self.graph.update_data(self.variable_x, self.variable_y, True)
def commit(self):
selection = self.graph.get_selection()
if self._embedding_data_object is not None and selection is not None:
inputs = {
'data_table': self.data_table_object,
'embedding': self._embedding_data_object,
'selection': selection.tolist(),
'x_tsne_var': self.variable_x.name,
'y_tsne_var': self.variable_y.name
}
func = partial(self.res.run_process, self._tsne_selection_slug,
**inputs)
self.run_task(self._tsne_selection_slug, func)
self.Outputs.selected_data.send(None)
def onDeleteWidget(self):
super().onDeleteWidget()
self._clear_plot()
self._clear_state()
def send_report(self):
if self.data is None:
return
def name(var):
return var and var.name
caption = report.render_items_vert(
(("Color", name(self.graph.attr_color)),
("Label", name(self.graph.attr_label)),
("Shape", name(self.graph.attr_shape)),
("Size", name(self.graph.attr_size)),
("Jittering", self.graph.jitter_size != 0
and "{} %".format(self.graph.jitter_size))))
self.report_plot()
if caption:
self.report_caption(caption)
def __init__(self):
super().__init__()
#: Effective data used for plot styling/annotations.
self.data = None # type: Optional[Orange.data.Table]
#: Input subset data table
self.subset_data = None # type: Optional[Orange.data.Table]
#: Input data table
self.signal_data = None
# resolwe variables
self.data_table_object = None # type: Optional[resolwe.Data]
self._tsne_slug = 't-sne'
self._tsne_selection_slug = 't-sne-selection'
self._embedding_data_object = None
self._embedding = None
self._embedding_clas_var = None
self.variable_x = ContinuousVariable("tsne-x")
self.variable_y = ContinuousVariable("tsne-y")
# threading
self._task = None # type: Optional[ResolweTask]
self._executor = ThreadExecutor()
self.res = ResolweHelper()
self._subset_mask = None # type: Optional[np.ndarray]
self._invalidated = False
self.pca_data = None
self._curve = None
self._data_metas = None
self.variable_x = ContinuousVariable("tsne-x")
self.variable_y = ContinuousVariable("tsne-y")
self.__update_loop = None
self.__in_next_step = False
self.__draw_similar_pairs = False
box = gui.vBox(self.controlArea, "t-SNE")
form = QFormLayout(labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow,
verticalSpacing=10)
form.addRow("Max iterations:",
gui.spin(box, self, "max_iter", 250, 2000, step=50))
form.addRow("Perplexity:",
gui.spin(box, self, "perplexity", 1, 100, step=1))
box.layout().addLayout(form)
gui.separator(box, 10)
self.runbutton = gui.button(box,
self,
"Run",
callback=self._run_embeding)
box = gui.vBox(self.controlArea, "PCA Preprocessing")
gui.hSlider(box,
self,
'pca_components',
label="Components: ",
minValue=2,
maxValue=50,
step=1) #, callback=self._initialize)
box = gui.vBox(self.mainArea, True, margin=0)
self.graph = OWMDSGraph(self,
box,
"MDSGraph",
view_box=MDSInteractiveViewBox)
box.layout().addWidget(self.graph.plot_widget)
self.plot = self.graph.plot_widget
g = self.graph.gui
box = g.point_properties_box(self.controlArea)
self.models = g.points_models
# Because sc data frequently has many genes,
# showing all attributes in combo boxes can cause problems
# QUICKFIX: Remove a separator and attributes from order
# (leaving just the class and metas)
for model in self.models:
model.order = model.order[:-2]
g.add_widgets(ids=[g.JitterSizeSlider], widget=box)
box = gui.vBox(self.controlArea, "Plot Properties")
g.add_widgets([
g.ShowLegend, g.ToolTipShowsAll, g.ClassDensity,
g.LabelOnlySelected
], box)
self.controlArea.layout().addStretch(100)
self.icons = gui.attributeIconDict
palette = self.graph.plot_widget.palette()
self.graph.set_palette(palette)
gui.rubber(self.controlArea)
self.graph.box_zoom_select(self.controlArea)
gui.auto_commit(self.controlArea, self, "auto_commit",
"Send Selection", "Send Automatically")
self.plot.getPlotItem().hideButtons()
self.plot.setRenderHint(QPainter.Antialiasing)
self.graph.jitter_continuous = True
class OWResolweFilter(widget.OWWidget):
name = "Resolwe Filter"
icon = 'icons/OWResolweFilter.svg'
description = "Filter cells/genes"
priority = 40
class Inputs:
data = widget.Input("Data", resolwe.Data)
class Outputs:
data = widget.Output("Data", resolwe.Data)
class Warning(widget.OWWidget.Warning):
invalid_range = widget.Msg(
"Negative values in input data.\n"
"This filter only makes sense for non-negative measurements "
"where 0 indicates a lack (of) and/or a neutral reading.")
sampling_in_effect = widget.Msg("Too many data points to display.\n"
"Sampling {} of {} data points.")
#: Filter mode.
#: Filter out rows/columns.
Cells, Genes = Cells, Genes
settings_version = 1
#: The selected filter mode
selected_filter_type = settings.Setting(Cells) # type: int
#: Selected filter statistics / QC measure indexed by filter_type
selected_filter_metric = settings.Setting(TotalCounts) # type: int
#: Augment the violin plot with a dot plot (strip plot) of the (non-zero)
#: measurement counts in Cells/Genes mode or data matrix values in Data
#: mode.
display_dotplot = settings.Setting(True) # type: bool
#: Is min/max range selection enable
limit_lower_enabled = settings.Setting(True) # type: bool
limit_upper_enabled = settings.Setting(True) # type: bool
#: The lower and upper selection limit for each filter type
thresholds = settings.Setting({
(Cells, DetectionCount): (0, 2**31 - 1),
(Cells, TotalCounts): (0, 2**31 - 1),
(Genes, DetectionCount): (0, 2**31 - 1),
(Genes, TotalCounts): (0, 2**31 - 1)
}) # type: Dict[Tuple[int, int], Tuple[float, float]]
auto_commit = settings.Setting(False) # type: bool
def __init__(self):
super().__init__()
self.data_table_object = None # type: Optional[resolwe.Data]
self._counts = None # type: Optional[np.ndarray]
self._counts_data_obj = None # type: Optional[resolwe.Data]
self._counts_slug = 'data-filter-counts' # type: str
self._selection_data_obj = None # type: Optional[resolwe.Data]
self._selection_slug = 'data-table-filter' # type: str
# threading
self._task = None # type: Optional[ResolweTask]
self._executor = ThreadExecutor()
self.res = ResolweHelper()
box = gui.widgetBox(self.controlArea, "Info")
self._info = QLabel(box)
self._info.setWordWrap(True)
self._info.setText("No data in input\n")
box.layout().addWidget(self._info)
box = gui.widgetBox(self.controlArea, "Filter Type", spacing=-1)
rbg = QButtonGroup(box, exclusive=True)
layout = QHBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
for id_ in [Cells, Genes]:
name, _, tip = FilterInfo[id_]
b = QRadioButton(name,
toolTip=tip,
checked=id_ == self.selected_filter_type)
rbg.addButton(b, id_)
layout.addWidget(b, stretch=10, alignment=Qt.AlignCenter)
box.layout().addLayout(layout)
rbg.buttonClicked[int].connect(self.set_filter_type)
self.filter_metric_cb = gui.comboBox(box,
self,
"selected_filter_metric",
callback=self._update_metric)
for id_ in [DetectionCount, TotalCounts]:
text, ttip = MeasureInfo[id_]
self.filter_metric_cb.addItem(text)
idx = self.filter_metric_cb.count() - 1
self.filter_metric_cb.setItemData(idx, ttip, Qt.ToolTipRole)
self.filter_metric_cb.setCurrentIndex(self.selected_filter_metric)
form = QFormLayout(labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow)
self._filter_box = box = gui.widgetBox(
self.controlArea, "Filter", orientation=form) # type: QGroupBox
self.threshold_stacks = (
QStackedWidget(enabled=self.limit_lower_enabled),
QStackedWidget(enabled=self.limit_upper_enabled),
)
finfo = np.finfo(np.float64)
for filter_ in [Cells, Genes]:
if filter_ in {Cells, Genes}:
minimum = 0.0
ndecimals = 1
metric = self.selected_filter_metric
else:
minimum = finfo.min
ndecimals = 3
metric = -1
spinlower = QDoubleSpinBox(
self,
minimum=minimum,
maximum=finfo.max,
decimals=ndecimals,
keyboardTracking=False,
)
spinupper = QDoubleSpinBox(
self,
minimum=minimum,
maximum=finfo.max,
decimals=ndecimals,
keyboardTracking=False,
)
lower, upper = self.thresholds.get((filter_, metric), (0, 0))
spinlower.setValue(lower)
spinupper.setValue(upper)
self.threshold_stacks[0].addWidget(spinlower)
self.threshold_stacks[1].addWidget(spinupper)
spinlower.valueChanged.connect(self._limitchanged)
spinupper.valueChanged.connect(self._limitchanged)
self.threshold_stacks[0].setCurrentIndex(self.selected_filter_type)
self.threshold_stacks[1].setCurrentIndex(self.selected_filter_type)
self.limit_lower_enabled_cb = cb = QCheckBox(
"Min", checked=self.limit_lower_enabled)
cb.toggled.connect(self.set_lower_limit_enabled)
cb.setAttribute(Qt.WA_LayoutUsesWidgetRect, True)
form.addRow(cb, self.threshold_stacks[0])
self.limit_upper_enabled_cb = cb = QCheckBox(
"Max", checked=self.limit_upper_enabled)
cb.toggled.connect(self.set_upper_limit_enabled)
cb.setAttribute(Qt.WA_LayoutUsesWidgetRect, True)
form.addRow(cb, self.threshold_stacks[1])
box = gui.widgetBox(self.controlArea, "View")
self._showpoints = gui.checkBox(box,
self,
"display_dotplot",
"Show data points",
callback=self._update_dotplot)
self.controlArea.layout().addStretch(10)
gui.auto_commit(self.controlArea, self, "auto_commit", "Commit")
self._view = pg.GraphicsView()
self._view.enableMouse(False)
self._view.setAntialiasing(True)
self._plot = plot = ViolinPlot()
self._plot.setDataPointsVisible(self.display_dotplot)
self._plot.setSelectionMode(
(ViolinPlot.Low if self.limit_lower_enabled else 0)
| (ViolinPlot.High if self.limit_upper_enabled else 0))
self._plot.selectionEdited.connect(self._limitchanged_plot)
self._view.setCentralWidget(self._plot)
self._plot.setTitle(FilterInfo[self.selected_filter_metric][1])
bottom = self._plot.getAxis("bottom") # type: pg.AxisItem
bottom.hide()
plot.setMouseEnabled(False, False)
plot.hideButtons()
self.mainArea.layout().addWidget(self._view)
self.addAction(
QAction("Select All",
self,
shortcut=QKeySequence.SelectAll,
triggered=self._select_all))
def cancel(self):
"""Cancel the current task (if any)."""
if self._task is not None:
self._task.cancel()
assert self._task.future.done()
# disconnect the `_task_finished` slot
self._task.watcher.done.disconnect(self.task_finished)
self._task = None
def run_task(self, slug, func):
if self._task is not None:
self.cancel()
assert self._task is None
self.progressBarInit()
self._task = ResolweTask(slug)
self._task.future = self._executor.submit(func)
self._task.watcher = FutureWatcher(self._task.future)
self._task.watcher.done.connect(self.task_finished)
@Slot(Future, name='Future')
def task_finished(self, future):
assert threading.current_thread() == threading.main_thread()
assert self._task is not None
assert self._task.future is future
assert future.done()
try:
future_result = future.result()
except Exception as ex:
# TODO: raise exceptions
raise ex
else:
if self._task.slug == self._counts_slug:
self._counts_data_obj = future_result
self._setup_plot(future_result)
elif self._task.slug == self._selection_slug:
self._selection_data_obj = future_result
self.Outputs.data.send(self._selection_data_obj)
self._update_info()
return self._selection_data_obj
finally:
self.progressBarFinished()
self._task = None
@Inputs.data
def set_data(self, data):
# type: (Optional[resolwe.Data]) -> None
self.clear()
self.data_table_object = data
if data is not None:
# self.res.get_object(id=data.id)
self._setup(data, self.filter_type())
def commit(self):
if self._counts_data_obj:
inputs = {
'data_table': self.data_table_object,
'counts': self._counts_data_obj,
'axis': self._counts_data_obj.input['axis']
}
if self.limit_upper_enabled:
inputs['upper_limit'] = self.limit_upper
if self.limit_lower_enabled:
inputs['lower_limit'] = self.limit_lower
func = partial(self.res.run_process, self._selection_slug,
**inputs)
self.run_task(self._selection_slug, func)
self.Outputs.data.send(None)
def _setup(self, data, filter_type):
self.clear()
axis = 1 if filter_type == Cells else 0
func = partial(self.res.run_process,
self._counts_slug,
data_table=data,
axis=axis,
measure=self.selected_filter_metric)
# move filter process in thread
self.run_task(self._counts_slug, func)
def _setup_plot(self, data_object):
# type: (resolwe.Data) -> None
filter_data = self.res.get_json(data_object, 'counts_json', 'counts')
axis_on_input = data_object.input['axis']
measure = self.selected_filter_metric
if axis_on_input == Cells:
title = "Cell Filter"
if measure == TotalCounts:
axis_label = "Total counts (library size)"
else:
axis_label = "Number of expressed genes"
else:
title = "Gene Filter"
if measure == TotalCounts:
axis_label = "Total counts"
else:
# TODO: Too long
axis_label = "Number of cells a gene is expressed in"
span = -1.0 # data span
x = np.asarray(filter_data)
if x.size:
span = np.ptp(x)
self._counts = x
self.Warning.sampling_in_effect.clear()
spinlow = self.threshold_stacks[0].widget(axis_on_input)
spinhigh = self.threshold_stacks[1].widget(axis_on_input)
if measure == TotalCounts:
if span > 0:
ndecimals = max(4 - int(np.floor(np.log10(span))), 1)
else:
ndecimals = 1
else:
ndecimals = 1
spinlow.setDecimals(ndecimals)
spinhigh.setDecimals(ndecimals)
if x.size:
xmin, xmax = np.min(x), np.max(x)
self.limit_lower = np.clip(self.limit_lower, xmin, xmax)
self.limit_upper = np.clip(self.limit_upper, xmin, xmax)
if x.size > 0:
# TODO: Need correction for lower bounded distribution (counts)
# Use reflection around 0, but gaussian_kde does not provide
# sufficient flexibility w.r.t bandwidth selection.
self._plot.setData(x, 1000)
self._plot.setBoundary(self.limit_lower, self.limit_upper)
ax = self._plot.getAxis("left") # type: pg.AxisItem
ax.setLabel(axis_label)
self._plot.setTitle(title)
self._update_info()
def sizeHint(self):
sh = super().sizeHint() # type: QSize
return sh.expandedTo(QSize(800, 600))
def set_filter_type(self, type_):
if self.selected_filter_type != type_:
assert type_ in (Cells, Genes), str(type_)
self.selected_filter_type = type_
self.threshold_stacks[0].setCurrentIndex(type_)
self.threshold_stacks[1].setCurrentIndex(type_)
if self.data_table_object is not None:
self._setup(self.data_table_object, type_)
def filter_type(self):
return self.selected_filter_type
def _update_metric(self):
if self.data_table_object is not None:
self._setup(
self.data_table_object,
self.selected_filter_type,
)
def set_upper_limit_enabled(self, enabled):
if enabled != self.limit_upper_enabled:
self.limit_upper_enabled = enabled
self.threshold_stacks[1].setEnabled(enabled)
self.limit_upper_enabled_cb.setChecked(enabled)
self._update_filter()
def set_lower_limit_enabled(self, enabled):
if enabled != self.limit_lower_enabled:
self.limit_lower_enabled = enabled
self.threshold_stacks[0].setEnabled(enabled)
self.limit_lower_enabled_cb.setChecked(enabled)
self._update_filter()
def _update_filter(self):
mode = 0
if self.limit_lower_enabled:
mode |= ViolinPlot.Low
if self.limit_upper_enabled:
mode |= ViolinPlot.High
self._plot.setSelectionMode(mode)
def _is_filter_enabled(self):
return self.limit_lower_enabled or self.limit_upper_enabled
def clear(self):
self._plot.clear()
self._selection_data_obj = None
self._counts_data_obj = None
self._counts = None
self._update_info()
self.Warning.clear()
def _update_info(self):
text = []
if self.data_table_object:
text.append('Input Data (object id): {}'.format(
self.data_table_object.id))
if self._selection_data_obj and self._counts_data_obj:
num_selected = self._selection_data_obj.output.get(
'num_selected', None)
axis = self._counts_data_obj.input.get('axis', None)
if num_selected is not None and axis is not None:
text.append('Output data ({instance}{s}): {num} '.format(
instance='gene' if axis == 0 else 'cell',
s='s' if num_selected > 0 else '',
num=num_selected))
self._info.setText('\n'.join(text))
def _select_all(self):
self.limit_lower = 0
self.limit_upper = 2**31 - 1
self._limitchanged()
def _update_dotplot(self):
self._plot.setDataPointsVisible(self.display_dotplot)
def current_filter_thresholds(self):
if self.selected_filter_type in {Cells, Genes}:
metric = self.selected_filter_metric
else:
metric = -1
return self.thresholds[self.selected_filter_type, metric]
def set_current_filter_thesholds(self, lower, upper):
if self.selected_filter_type in {Cells, Genes}:
metric = self.selected_filter_metric
else:
metric = -1
self.thresholds[self.selected_filter_type, metric] = (lower, upper)
@property
def limit_lower(self):
return self.current_filter_thresholds()[0]
@limit_lower.setter
def limit_lower(self, value):
_, upper = self.current_filter_thresholds()
self.set_current_filter_thesholds(value, upper)
stacklower, _ = self.threshold_stacks
sb = stacklower.widget(self.selected_filter_type)
# prevent changes due to spin box rounding
sb.setValue(value)
@property
def limit_upper(self):
return self.current_filter_thresholds()[1]
@limit_upper.setter
def limit_upper(self, value):
lower, _ = self.current_filter_thresholds()
self.set_current_filter_thesholds(lower, value)
_, stackupper = self.threshold_stacks
sb = stackupper.widget(self.selected_filter_type)
sb.setValue(value)
@Slot()
def _limitchanged(self):
# Low/high limit changed via the spin boxes
stacklow, stackhigh = self.threshold_stacks
filter_ = self.selected_filter_type
lower = stacklow.widget(filter_).value()
upper = stackhigh.widget(filter_).value()
self.set_current_filter_thesholds(lower, upper)
if self._counts is not None and self._counts.size:
xmin = np.min(self._counts)
xmax = np.max(self._counts)
self._plot.setBoundary(np.clip(lower, xmin, xmax),
np.clip(upper, xmin, xmax))
def _limitchanged_plot(self):
# Low/high limit changed via the plot
if self._counts is not None:
newlower, newupper = self._plot.boundary()
filter_ = self.selected_filter_type
lower, upper = self.current_filter_thresholds()
stacklow, stackhigh = self.threshold_stacks
spin_lower = stacklow.widget(filter_)
spin_upper = stackhigh.widget(filter_)
# do rounding to match the spin box's precision
if self.limit_lower_enabled:
newlower = round(newlower, spin_lower.decimals())
else:
newlower = lower
if self.limit_upper_enabled:
newupper = round(newupper, spin_upper.decimals())
else:
newupper = upper
if self.limit_lower_enabled and newlower != lower:
self.limit_lower = newlower
if self.limit_upper_enabled and newupper != upper:
self.limit_upper = newupper
self._plot.setBoundary(newlower, newupper)
def onDeleteWidget(self):
self.data_table_object = None
self.clear()
self._plot.close()
super().onDeleteWidget()
@classmethod
def migrate_settings(cls, settings, version):
if (version is None or version < 2) and \
("limit_lower" in settings and "limit_upper" in settings):
# v2 changed limit_lower, limit_upper to per filter limits stored
# in a single dict
lower = settings.pop("limit_lower")
upper = settings.pop("limit_upper")
settings["thresholds"] = {
(Cells, TotalCounts): (lower, upper),
(Cells, DetectionCount): (lower, upper),
(Genes, TotalCounts): (lower, upper),
(Genes, DetectionCount): (lower, upper),
}
if version == 2:
thresholds = settings["thresholds"]
c = thresholds.pop(Cells)
g = thresholds.pop(Genes)
thresholds = {
(Cells, TotalCounts): c,
(Cells, DetectionCount): c,
(Genes, TotalCounts): g,
(Genes, DetectionCount): g,
}
settings["thresholds"] = thresholds
def __init__(self):
super().__init__()
self.data_table_object = None # type: Optional[resolwe.Data]
self._counts = None # type: Optional[np.ndarray]
self._counts_data_obj = None # type: Optional[resolwe.Data]
self._counts_slug = 'data-filter-counts' # type: str
self._selection_data_obj = None # type: Optional[resolwe.Data]
self._selection_slug = 'data-table-filter' # type: str
# threading
self._task = None # type: Optional[ResolweTask]
self._executor = ThreadExecutor()
self.res = ResolweHelper()
box = gui.widgetBox(self.controlArea, "Info")
self._info = QLabel(box)
self._info.setWordWrap(True)
self._info.setText("No data in input\n")
box.layout().addWidget(self._info)
box = gui.widgetBox(self.controlArea, "Filter Type", spacing=-1)
rbg = QButtonGroup(box, exclusive=True)
layout = QHBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
for id_ in [Cells, Genes]:
name, _, tip = FilterInfo[id_]
b = QRadioButton(name,
toolTip=tip,
checked=id_ == self.selected_filter_type)
rbg.addButton(b, id_)
layout.addWidget(b, stretch=10, alignment=Qt.AlignCenter)
box.layout().addLayout(layout)
rbg.buttonClicked[int].connect(self.set_filter_type)
self.filter_metric_cb = gui.comboBox(box,
self,
"selected_filter_metric",
callback=self._update_metric)
for id_ in [DetectionCount, TotalCounts]:
text, ttip = MeasureInfo[id_]
self.filter_metric_cb.addItem(text)
idx = self.filter_metric_cb.count() - 1
self.filter_metric_cb.setItemData(idx, ttip, Qt.ToolTipRole)
self.filter_metric_cb.setCurrentIndex(self.selected_filter_metric)
form = QFormLayout(labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow)
self._filter_box = box = gui.widgetBox(
self.controlArea, "Filter", orientation=form) # type: QGroupBox
self.threshold_stacks = (
QStackedWidget(enabled=self.limit_lower_enabled),
QStackedWidget(enabled=self.limit_upper_enabled),
)
finfo = np.finfo(np.float64)
for filter_ in [Cells, Genes]:
if filter_ in {Cells, Genes}:
minimum = 0.0
ndecimals = 1
metric = self.selected_filter_metric
else:
minimum = finfo.min
ndecimals = 3
metric = -1
spinlower = QDoubleSpinBox(
self,
minimum=minimum,
maximum=finfo.max,
decimals=ndecimals,
keyboardTracking=False,
)
spinupper = QDoubleSpinBox(
self,
minimum=minimum,
maximum=finfo.max,
decimals=ndecimals,
keyboardTracking=False,
)
lower, upper = self.thresholds.get((filter_, metric), (0, 0))
spinlower.setValue(lower)
spinupper.setValue(upper)
self.threshold_stacks[0].addWidget(spinlower)
self.threshold_stacks[1].addWidget(spinupper)
spinlower.valueChanged.connect(self._limitchanged)
spinupper.valueChanged.connect(self._limitchanged)
self.threshold_stacks[0].setCurrentIndex(self.selected_filter_type)
self.threshold_stacks[1].setCurrentIndex(self.selected_filter_type)
self.limit_lower_enabled_cb = cb = QCheckBox(
"Min", checked=self.limit_lower_enabled)
cb.toggled.connect(self.set_lower_limit_enabled)
cb.setAttribute(Qt.WA_LayoutUsesWidgetRect, True)
form.addRow(cb, self.threshold_stacks[0])
self.limit_upper_enabled_cb = cb = QCheckBox(
"Max", checked=self.limit_upper_enabled)
cb.toggled.connect(self.set_upper_limit_enabled)
cb.setAttribute(Qt.WA_LayoutUsesWidgetRect, True)
form.addRow(cb, self.threshold_stacks[1])
box = gui.widgetBox(self.controlArea, "View")
self._showpoints = gui.checkBox(box,
self,
"display_dotplot",
"Show data points",
callback=self._update_dotplot)
self.controlArea.layout().addStretch(10)
gui.auto_commit(self.controlArea, self, "auto_commit", "Commit")
self._view = pg.GraphicsView()
self._view.enableMouse(False)
self._view.setAntialiasing(True)
self._plot = plot = ViolinPlot()
self._plot.setDataPointsVisible(self.display_dotplot)
self._plot.setSelectionMode(
(ViolinPlot.Low if self.limit_lower_enabled else 0)
| (ViolinPlot.High if self.limit_upper_enabled else 0))
self._plot.selectionEdited.connect(self._limitchanged_plot)
self._view.setCentralWidget(self._plot)
self._plot.setTitle(FilterInfo[self.selected_filter_metric][1])
bottom = self._plot.getAxis("bottom") # type: pg.AxisItem
bottom.hide()
plot.setMouseEnabled(False, False)
plot.hideButtons()
self.mainArea.layout().addWidget(self._view)
self.addAction(
QAction("Select All",
self,
shortcut=QKeySequence.SelectAll,
triggered=self._select_all))
class OWResolweDataSets(widget.OWWidget):
name = "Resolwe Datasets"
description = "Load a dataset from resolwe based server"
icon = "icons/OWResolweDataSets.svg"
priority = 30
auto_commit = settings.Setting(True)
DATA_TYPE = 'singlecell'
DESCRIPTOR_SCHEMA = 'data_info'
class Error(widget.OWWidget.Error):
no_remote_datasets = Msg("Could not fetch dataset list")
class Warning(widget.OWWidget.Warning):
only_local_datasets = Msg("pass")
class Outputs:
data_object = Output("Data Object", Data)
class Inputs:
data_table = Input("Data", Table)
def __init__(self):
super().__init__()
info_box = gui.widgetBox(self.controlArea, "Info")
self.info_label = QLabel()
info_box.layout().addWidget(self.info_label)
self.res = ResolweHelper()
data_objects = self.res.list_data_objects(self.DATA_TYPE)
descriptor_schema = self.res.get_descriptor_schema(
self.DESCRIPTOR_SCHEMA)
self.res_widget = ResolweDataWidget(data_objects, descriptor_schema)
self.res_widget.view.selectionModel().selectionChanged.connect(
self.commit)
self.res_widget.set_target_column(self.res_widget.header.target)
self.__assign_delegates()
self.udpdate_info_box()
self.mainArea.layout().addWidget(self.res_widget)
self.controlArea.layout().addStretch(10)
gui.auto_commit(self.controlArea, self, "auto_commit", "&Commit")
print(os.environ.get('RESOLWE_HOST_URL'))
print(os.environ.get('RESOLWE_API_USERNAME'))
print(os.environ.get('RESOLWE_API_PASSWORD'))
def __assign_delegates(self):
self.res_widget.view.setItemDelegateForColumn(
self.res_widget.header.file_size, SizeDelegate(self))
self.res_widget.view.setItemDelegateForColumn(
self.res_widget.header.cells, NumericalDelegate(self))
self.res_widget.view.setItemDelegateForColumn(
self.res_widget.header.genes, NumericalDelegate(self))
def udpdate_info_box(self):
if self.res_widget.data_objects:
self.info_label.setText('Data objects on server: {}'.format(
len(self.res_widget.data_objects)))
@Inputs.data_table
def handle_input(self, data):
# upload file
self.res.upload_data_table(data)
# fetch data object and reconstruct data model
self.res_widget.data_objects = self.res.list_data_objects(
self.DATA_TYPE)
def commit(self):
sel_data_obj = self.res_widget.selected_data_object()
assert isinstance(sel_data_obj, Data)
self.Outputs.data_object.send(sel_data_obj)
def sizeHint(self):
return QSize(900, 600)