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.
# 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.
