def threshold_gate(self, channel_name=''): if not channel_name: channel_name = self.channel_names[0] # Check if file already exists if CHECK_IF_FILE_EXIST: if self.check_if_images_exist('threshold_gate'): return True # Create a threshold gates y2_gate = ThresholdGate(1000.0, channel_name, region='above') # Gate gated_sample = self.sample.gate(y2_gate) # Plot ax1 = subplot(121) self.sample.plot(channel_name, gates=[y2_gate], bins=self.bins, alpha=0.9) y2_gate.plot(color='k', linewidth=4, linestyle='-') title('Original Sample') ax2 = subplot(122, sharey=ax1, sharex=ax1) gated_sample.plot(channel_name, gates=[y2_gate], bins=self.bins, color='y', alpha=0.9) title('Gated Sample') tight_layout() png_file = os.path.join(SHARED_PLOTTING_DIR, self.get_file_name('threshold_gate.png')) print(png_file) grid(True) savefig(png_file) self.response['threshold_gate'] = self.get_file_name( 'threshold_gate.png')
# Locate sample data included with this package datadir = os.path.join(FlowCytometryTools.__path__[0], 'tests', 'data', 'Plate01') datafile = os.path.join(datadir, 'RFP_Well_A3.fcs') # datafile = '[insert path to your own fcs file]' # Load data tsample = FCMeasurement(ID='Test Sample', datafile=datafile) tsample = tsample.transform('hlog', channels=['Y2-A', 'B1-A', 'V2-A'], b=500.0) # Create a threshold gates y2_gate = ThresholdGate(1000.0, 'Y2-A', region='above') # Gate gated_sample = tsample.gate(y2_gate) # Plot ax1 = subplot(121); tsample.plot('Y2-A', gates=[y2_gate], bins=100, alpha=0.9); y2_gate.plot(color='k', linewidth=4, linestyle='-') title('Original Sample'); ax2 = subplot(122, sharey=ax1, sharex=ax1); gated_sample.plot('Y2-A', gates=[y2_gate], bins=100, color='y', alpha=0.9); title('Gated Sample'); tight_layout() #show() # <-- Uncomment when running as a script.