def setUp(self):
ImportedDataTest.setUp(self)
self.ex = flow.ThresholdOp(name="T", channel="Y2-A",
threshold=500).apply(self.ex)
self.ex = flow.ChannelStatisticOp(name="ByDox",
channel="Y2-A",
by=['Dox'],
function=flow.geom_mean).apply(
self.ex)
self.ex = flow.ChannelStatisticOp(name="ByDoxWell",
channel="Y2-A",
by=['Dox', 'Well'],
function=flow.geom_mean).apply(
self.ex)
self.ex = flow.ChannelStatisticOp(name="ByDox",
channel="Y2-A",
by=['Dox'],
function=flow.geom_sd_range).apply(
self.ex)
self.ex = flow.ChannelStatisticOp(name="ByDoxWell",
channel="Y2-A",
by=['Dox', 'Well'],
function=flow.geom_sd_range).apply(
self.ex)
def setUp(self):
super().setUp()
self.ex = flow.ThresholdOp(name="T", channel="Y2-A",
threshold=500).apply(self.ex)
self.ex = flow.ChannelStatisticOp(name="ByDox",
by=['Dox', 'T'],
channel="Y2-A",
function=len).apply(self.ex)
def setUp(self):
self.cwd = os.path.dirname(os.path.abspath(__file__)) + "/data/Plate01/"
tube1 = flow.Tube(file = self.cwd + 'RFP_Well_A3.fcs', conditions = {"Dox" : 10.0})
tube2 = flow.Tube(file= self.cwd + 'CFP_Well_A4.fcs', conditions = {"Dox" : 1.0})
import_op = flow.ImportOp(conditions = {"Dox" : "float"},
tubes = [tube1, tube2])
self.ex = import_op.apply()
self.gate = flow.ThresholdOp(name = "Threshold",
channel = "Y2-A",
threshold = 500)
def setUp(self):
self.cwd = os.path.dirname(os.path.abspath(__file__)) + "/data/Plate01/"
tube1 = flow.Tube(file = self.cwd + 'RFP_Well_A3.fcs', conditions = {"Dox" : 10.0})
tube2 = flow.Tube(file= self.cwd + 'CFP_Well_A4.fcs', conditions = {"Dox" : 1.0})
import_op = flow.ImportOp(conditions = {"Dox" : "float"},
tubes = [tube1, tube2])
self.ex = import_op.apply()
self.ex = flow.ThresholdOp(name = "T",
channel = "Y2-A",
threshold = 500).apply(self.ex)
self.ex = flow.ChannelStatisticOp(name = "ByDox",
by = ['Dox', 'T'],
channel = "Y2-A",
function = len).apply(self.ex)
def setUp(self):
ImportedDataTest.setUp(self)
self.ex = flow.ThresholdOp(name = "T",
channel = "Y2-A",
threshold = 500).apply(self.ex)
self.ex = flow.ChannelStatisticOp(name = "ByDox",
channel = "Y2-A",
by = ['T', 'Dox'],
function = flow.geom_mean).apply(self.ex)
self.ex = flow.ChannelStatisticOp(name = "ByDox",
channel = "Y2-A",
by = ['T', 'Dox'],
function = flow.geom_sd_range).apply(self.ex)
self.view = flow.Stats1DView(statistic = ("ByDox", "geom_mean"),
error_statistic = ("ByDox", "geom_sd_range"),
variable = "Dox",
huefacet = "T")
def setUp(self):
self.cwd = os.path.dirname(
os.path.abspath(__file__)) + "/data/Plate01/"
tube1 = flow.Tube(file=self.cwd + 'RFP_Well_A3.fcs',
conditions={"Dox": 10.0})
tube2 = flow.Tube(file=self.cwd + 'CFP_Well_A4.fcs',
conditions={"Dox": 1.0})
import_op = flow.ImportOp(conditions={"Dox": "float"},
tubes=[tube1, tube2])
ex = import_op.apply()
# this works so much better on transformed data
logicle = flow.LogicleTransformOp()
logicle.name = "Logicle transformation"
logicle.channels = ['V2-A', 'Y2-A', 'B1-A']
logicle.estimate(ex)
self.ex = logicle.apply(ex)
self.gate = flow.ThresholdOp(name="Threshold",
channel="Y2-A",
threshold=0.4)
util.expand_class_attributes(DensityView)
util.expand_method_parameters(DensityView, DensityView.plot)
if __name__ == '__main__':
import cytoflow as flow
tube1 = flow.Tube(file='../../cytoflow/tests/data/Plate01/RFP_Well_A3.fcs',
conditions={"Dox": 10.0})
tube2 = flow.Tube(file='../../cytoflow/tests/data/Plate01/CFP_Well_A4.fcs',
conditions={"Dox": 1.0})
ex = flow.ImportOp(conditions={"Dox": "float"}, tubes=[tube1, tube2])
thresh = flow.ThresholdOp()
thresh.name = "Y2-A+"
thresh.channel = 'Y2-A'
thresh.threshold = 200.0
ex2 = thresh.apply(ex)
scatter = flow.ScatterplotView()
scatter.name = "Scatter"
scatter.xchannel = "FSC-A"
scatter.ychannel = "SSC-A"
scatter.xscale = "logicle"
scatter.yscale = "logicle"
scatter.huefacet = 'Dox'
plt.ioff()
def setUp(self):
super().setUp()
self.ex = flow.ThresholdOp(name="T", channel="Y2-A",
threshold=500).apply(self.ex)
def setUp(self):
super().setUp()
self.gate = flow.ThresholdOp(name = "Threshold",
channel = "Y2-A",
threshold = 500)