class Waterfall(QWidget, waterfall.Ui_Waterfall):
plot_settings_signal = QtCore.pyqtSignal(list) #send list of plotting params
updated_rectangles_signal = QtCore.pyqtSignal(list) #send list of updated artists for redrawing
def __init__(self, parent):
super(Waterfall,self).__init__(parent)
self.setupUi(self)
self.get_settings()
self.send_settings()
#Button functions
self.btn_apply_general_settings.clicked.connect(self.send_settings)
self.btn_apply_keys_and_colors_settings.clicked.connect(self.send_settings)
self.patient_tree = self.create_patient_tree()
self.data_viewer_container.addWidget(self.patient_tree)
self.btn_color_test.clicked.connect(self.get_color)
def get_color(self):
self.color = QColorDialog.getColor() #returns a color object
print(color)
def get_settings(self):
try:
with shelve.open('WaterfallSettings') as shelfFile:
self.keys_and_colors = shelfFile['keys_and_colors']
shelfFile.close()
except:
#set and use default settings
self.keys_and_colors = {
'CR':'#03945D',
'PR':'#B1EE97',
'PD':'#FF6F69',
'SD':'#707070'}
with shelve.open('WaterfallSettings') as shelfFile:
shelfFile['keys_and_colors'] = self.keys_and_colors
shelfFile.close()
def on_waterfall_data_signal(self,signal):
self.waterfall_data = signal['waterfall_data'] #pandas dataframe
def on_generated_rectangles_signal(self,signal):
self.rectangles_received = signal[0]
self.add_items() #display in table
self.btn_apply_general_settings.setEnabled(True)
self.btn_finalize_plot.setEnabled(True)
self.btn_apply_keys_and_colors_settings.setEnabled(True)
def send_settings(self):
'''
Emit both general plot settings, and color labeling settings. These are the settings to be used when the plot is created.
'''
self.general_settings = [
self.plot_title.text(),
self.x_label.text(),
self.y_label.text(),
[self.twenty_percent_line.isChecked(),
self.thirty_percent_line.isChecked(),
self.zero_percent_line.isChecked()],
[self.display_responses_as_text.isChecked(),
self.display_responses_as_color.isChecked(),
self.display_no_responses.isChecked()],
self.include_table.isChecked(),
self.show_cancer_type.isChecked()
]
self.plot_settings_signal.emit(self.general_settings)
def create_patient_tree(self):
'''
Create QTreeWidget populated with a patient's data for the DataEntry dialog.
Assumes that self.temp_patient is the patient of interest and that the variable belongs to the dialog.
'''
self.tree = QTreeWidget()
self.root = self.tree.invisibleRootItem()
self.headers = [
'Patient #',
'Best response %',
'Response',
'Cancer',
'Color key',
]
self.headers_item = QTreeWidgetItem(self.headers)
self.tree.setColumnCount(len(self.headers))
self.tree.setHeaderItem(self.headers_item)
self.root.setExpanded(True)
self.tree.header().setSectionResizeMode(QHeaderView.ResizeToContents)
self.tree.header().setStretchLastSection(False)
return self.tree
def add_items(self):
'''
Populate viewing tree
'''
self.tree.clear() #clear prior to entering items, prevent aggregation
i=0
for rect in self.rectangles_received:
#populate editable tree with rect data
self.rect_item = QTreeWidgetItem(self.root)
self.rect_params = [
self.waterfall_data['Patient number'][i],
rect.get_height(),
self.waterfall_data['Overall response'][i],
self.waterfall_data['Cancer'][i]
]
for col in range(0,4):
self.rect_item.setText(col,str(self.rect_params[col]))
self.rect_item.setTextAlignment(col,4)
self.tree.setItemWidget(self.rect_item, 4, CustomCombo(self,self.keys_and_colors,self.waterfall_data['Overall response'][i]))
self.rect_item.setFlags(self.rect_item.flags() | QtCore.Qt.ItemIsEditable)
i+=1
if self.display_no_responses
for child_item in self.tree.children():
def on_updated_tree_item(self):
#update the rectangle which was edited
pass
class WaterfallPlotter(QWidget):
generated_rectangles_signal = QtCore.pyqtSignal(list) #send list of rects for data display in tree
def __init__(self,parent):
super(WaterfallPlotter,self).__init__(parent)
self.get_settings()
self.settings_update = False
self.figure = plt.figure()
self.canvas = FigureCanvas(self.figure)
self.toolbar = NavigationToolbar(self.canvas,self)
self.btn_plot = QPushButton('Default Plot')
self.btn_plot.clicked.connect(self.default_plot)
self.layout = QVBoxLayout()
self.layout.addWidget(self.toolbar)
self.layout.addWidget(self.canvas)
self.layout.addWidget(self.btn_plot)
self.setLayout(self.layout)
def on_waterfall_data_signal(self,signal):
self.waterfall_data = signal['waterfall_data'] #pandas dataframe
self.btn_plot.setEnabled(True)
def get_settings(self):
try:
with shelve.open('WaterfallSettings') as shelfFile:
self.keys_and_colors = shelfFile['keys_and_colors']
shelfFile.close()
except:
#set and use default settings
self.keys_and_colors = {
'CR':'#03945D',
'PR':'#B1EE97',
'PD':'#FF6F69',
'SD':'#707070'}
with shelve.open('WaterfallSettings') as shelfFile:
shelfFile['keys_and_colors'] = self.keys_and_colors
shelfFile.close()
def on_general_settings_signal(self,signal):
self.gen_settings = signal
self.settings_update = True
self.default_plot()
def get_bar_colors(self,responses):
return [self.keys_and_colors[x] for x in responses]
def default_plot(self):
'''
Plot waterfall data
'''
self.figure.clear()
self.rect_locations = np.arange(len(self.waterfall_data['Best response percent change']))
self.ax = self.figure.add_subplot(111)
self.bar_colors = self.get_bar_colors(self.waterfall_data['Overall response'])
if self.settings_update == False:
self.ax.tick_params(
axis='x', # changes apply to the x-axis
which='both', # both major and minor ticks are affected
bottom='on', # ticks along the bottom edge are off
top='on', # ticks along the top edge are off
labelbottom='on'
) # labels along the bottom edge are off
self.ax.axhline(y=20, linestyle='--', c='k', alpha=0.5, lw=2.0, label='twenty_percent')
self.ax.axhline(y=-30, linestyle='--', c='k', alpha=0.5, lw=2.0, label='thirty_percent')
self.ax.axhline(y=0, c='k', alpha=1, lw=2.0, label='zero_percent')
self.ax.grid(color = 'k', axis = 'y', alpha=0.25)
self.rects = self.ax.bar(self.rect_locations, self.waterfall_data['Best response percent change'], color=self.bar_colors)
else:
#settings were updated, we received them and stored in variable self.gen_settings
self.ax.set_title(self.gen_settings[0])
self.ax.set_xlabel(self.gen_settings[1])
self.ax.set_ylabel(self.gen_settings[2])
if self.gen_settings[3][0]:
self.ax.axhline(y=20, linestyle='--', c='k', alpha=0.5, lw=2.0, label='twenty_percent')
if self.gen_settings[3][1]:
self.ax.axhline(y=-30, linestyle='--', c='k', alpha=0.5, lw=2.0, label='thirty_percent')
if self.gen_settings[3][2]:
self.ax.axhline(y=0, c='k', alpha=1, lw=2.0, label='zero_percent')
if self.gen_settings[4][0] and ~self.gen_settings[6]:
#show responses as labels, default color bars
#legend depends on user specified keys
self.rects = self.ax.bar(self.rect_locations, self.waterfall_data['Best response percent change'])
self.add_labels(self.ax, self.rects, self.waterfall_data, 1)
elif self.gen_settings[4][1]:
#color bars with response type
self.rects = self.ax.bar(self.rect_locations, self.waterfall_data['Best response percent change'], color=self.bar_colors)
self.patches = []
for key in self.keys_and_colors.keys():
self.patches.append(mpatches.Patch(color = self.keys_and_colors[key],label=key))
self.ax.legend(handles=self.patches)
else:
self.rects = self.ax.bar(self.rect_locations, self.waterfall_data['Best response percent change'])
if self.gen_settings[5]:
self.plot_table()
if self.gen_settings[6] and ~self.gen_settings[4][0]:
self.add_labels(self.ax, self.rects, self.waterfall_data, 0)
self.ax.grid(color = 'k', axis = 'y', alpha=0.25)
self.canvas.draw()
self.generated_rectangles_signal.emit([self.rects])
def plot_table(self):
rows = ['%s' % x for x in self.waterfall_data.keys()]
rows = rows[4:] #skip first three, they are the 4 standard headers, rest are table rows
columns = self.waterfall_data['Patient number'] #patient numbers
cell_text = []
for row in rows:
cell_text_temp = []
for col in range(len(columns)):
cell_text_temp.append(self.waterfall_data[row][col])
cell_text.append(cell_text_temp)
the_table = self.ax.table(cellText=cell_text, rowLabels=rows, colLabels=columns, loc='bottom', cellLoc='center', colLoc='center')
plt.subplots_adjust(bottom=0.15,left=0.5)
self.ax.set_xlim(-0.5,len(columns)-0.5)
self.ax.tick_params(
axis='x', # changes apply to the x-axis
which='both', # both major and minor ticks are affected
bottom='off', # ticks along the bottom edge are off
top='off', # ticks along the top edge are off
labelbottom='off'
) # labels along the bottom edge are off
def update_plot(self):
'''
TODO
'''
pass
def add_labels(self, ax, rects, waterfall_data, label_type):
'''
Add labels above/below bars. label_type == 1 --> display responses; == 0 --> display cancer type
'''
i = 0
if label_type:
for rect in rects:
height = rect.get_height()
if height >= 0:
valign = 'bottom'
else:
valign = 'top'
ax.text(rect.get_x() + rect.get_width()/2., height,
'%s' % waterfall_data['Overall response'][i], ha='center', va=valign)
i+=1
else:
for rect in rects:
height = rect.get_height()
if height >= 0:
valign = 'top'
hgt = -1
else:
valign = 'bottom'
hgt = 1
ax.text(rect.get_x() + rect.get_width()/2., hgt,
'%s' % waterfall_data['Cancer'][i], ha='center', va=valign, rotation='vertical')
i+=1
class Waterfall(QWidget, waterfall.Ui_Waterfall):
plot_settings_signal = QtCore.pyqtSignal(list) #send list of plotting params
updated_rectangles_signal = QtCore.pyqtSignal(list) #send list of updated artists for redrawing
def __init__(self, parent):
super(Waterfall,self).__init__(parent)
self.setupUi(self)
self.get_settings()
self.send_settings()
#Button functions
self.btn_apply_general_settings.clicked.connect(self.send_settings)
self.btn_apply_keys_and_colors_settings.clicked.connect(self.send_settings)
self.patient_tree = self.create_patient_tree()
self.data_viewer_container.addWidget(self.patient_tree)
self.btn_color_test.clicked.connect(self.get_color)
def get_color(self):
self.color = QColorDialog.getColor() #returns a color object
print(color)
def get_settings(self):
try:
with shelve.open('WaterfallSettings') as shelfFile:
self.keys_and_colors = shelfFile['keys_and_colors']
shelfFile.close()
except:
#set and use default settings
self.keys_and_colors = {
'CR':'#03945D',
'PR':'#B1EE97',
'PD':'#FF6F69',
'SD':'#707070'}
with shelve.open('WaterfallSettings') as shelfFile:
shelfFile['keys_and_colors'] = self.keys_and_colors
shelfFile.close()
def on_waterfall_data_signal(self,signal):
self.waterfall_data = signal['waterfall_data'] #pandas dataframe
def on_generated_rectangles_signal(self,signal):
self.rectangles_received = signal[0]
self.add_items() #display in table
self.btn_apply_general_settings.setEnabled(True)
self.btn_finalize_plot.setEnabled(True)
self.btn_apply_keys_and_colors_settings.setEnabled(True)
def send_settings(self):
'''
Emit both general plot settings, and color labeling settings. These are the settings to be used when the plot is created.
'''
self.general_settings = [
self.plot_title.text(),
self.x_label.text(),
self.y_label.text(),
[self.twenty_percent_line.isChecked(),
self.thirty_percent_line.isChecked(),
self.zero_percent_line.isChecked()],
[self.display_responses_as_text.isChecked(),
self.display_responses_as_color.isChecked(),
self.display_no_responses.isChecked()],
self.include_table.isChecked(),
self.show_cancer_type.isChecked()
]
self.plot_settings_signal.emit(self.general_settings)
def create_patient_tree(self):
'''
Create QTreeWidget populated with a patient's data for the DataEntry dialog.
Assumes that self.temp_patient is the patient of interest and that the variable belongs to the dialog.
'''
self.tree = QTreeWidget()
self.root = self.tree.invisibleRootItem()
self.headers = [
'Patient #',
'Best response %',
'Response',
'Cancer',
'Color key',
]
self.headers_item = QTreeWidgetItem(self.headers)
self.tree.setColumnCount(len(self.headers))
self.tree.setHeaderItem(self.headers_item)
self.root.setExpanded(True)
self.tree.header().setSectionResizeMode(QHeaderView.ResizeToContents)
self.tree.header().setStretchLastSection(False)
return self.tree
def add_items(self):
'''
Populate viewing tree
'''
self.tree.clear() #clear prior to entering items, prevent aggregation
i=0
for rect in self.rectangles_received:
#populate editable tree with rect data
self.rect_item = QTreeWidgetItem(self.root)
self.rect_params = [
self.waterfall_data['Patient number'][i],
rect.get_height(),
self.waterfall_data['Overall response'][i],
self.waterfall_data['Cancer'][i]
]
for col in range(0,4):
self.rect_item.setText(col,str(self.rect_params[col]))
self.rect_item.setTextAlignment(col,4)
self.tree.setItemWidget(self.rect_item, 4, CustomCombo(self,self.keys_and_colors,self.waterfall_data['Overall response'][i]))
self.rect_item.setFlags(self.rect_item.flags() | QtCore.Qt.ItemIsEditable)
i+=1
if ~self.display_no_responses and ~self.display_responses_as_color:
for child_item in self.tree.children():
def on_updated_tree_item(self):
#update the rectangle which was edited
pass
