def setUp(self):
ImportedDataTest.setUp(self)
self.ex = flow.ChannelStatisticOp(name="Y",
channel="Y2-A",
by=['Well', 'Dox'],
function=flow.geom_mean).apply(
self.ex)
self.ex = flow.ChannelStatisticOp(name="Y",
channel="Y2-A",
by=['Well', 'Dox'],
function=flow.geom_sd_range).apply(
self.ex)
self.ex = flow.ChannelStatisticOp(name="V",
channel="V2-A",
by=['Well', 'Dox'],
function=flow.geom_mean).apply(
self.ex)
self.ex = flow.ChannelStatisticOp(name="V",
channel="V2-A",
by=['Well', 'Dox'],
function=flow.geom_sd_range).apply(
self.ex)
self.view = flow.Stats2DView(xstatistic=("Y", "geom_mean"),
x_error_statistic=("Y", "geom_sd_range"),
ystatistic=("V", "geom_mean"),
y_error_statistic=("V", "geom_sd_range"),
variable="Dox",
huefacet="Well")
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 testBadSet(self):
self.ex = flow.ChannelStatisticOp(name="Y_bad",
channel="Y2-A",
by=['Well'],
function=flow.geom_sd_range).apply(
self.ex)
def testStats2D(self):
import numpy as np
ex2 = flow.ChannelStatisticOp(name="StatsV",
by=["Dox"],
channel="V2-A",
function=np.mean).apply(self.ex)
ex3 = flow.ChannelStatisticOp(name="StatsY",
by=["Dox"],
channel="Y2-A",
function=np.mean).apply(ex2)
flow.Stats2DView(xstatistic=("StatsV", "mean"),
ystatistic=("StatsY", "mean"),
variable="Dox").plot(ex3)
def testTuple(self):
ex1 = flow.ChannelStatisticOp(name="ByDox",
channel="Y2-A",
by=['T'],
function=flow.geom_sd_range).apply(
self.ex)
ex2 = flow.ChannelStatisticOp(name="ByDox",
channel="Y2-A",
by=['T', 'Dox'],
function=flow.geom_sd_range).apply(
self.ex)
self.assertEqual(
type(ex1.statistics[('ByDox', 'geom_sd_range')].iloc[0]),
type(ex2.statistics[('ByDox', 'geom_sd_range')].iloc[0]))
def testErrorStat(self):
self.ex = flow.ChannelStatisticOp(name="ByDox",
by=['Dox', 'Well'],
channel="Y2-A",
function=util.geom_sd_range).apply(
self.ex)
self.view.error_statistic = ("ByDox", "geom_sd_range")
self.view.plot(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 testBadFunction(self):
op = flow.ChannelStatisticOp(name="ByDox",
by=['T'],
channel="Y2-A",
subset="Dox == 10.0",
function=lambda x: len(x) / 0.0)
with self.assertRaises(util.CytoflowOpError):
op.apply(self.ex)
def testSubset(self):
ex = flow.ChannelStatisticOp(name="ByDox",
by=['T'],
channel="Y2-A",
subset="Dox == 10.0",
function=len).apply(self.ex)
stat = ex.statistics[("ByDox", "len")]
self.assertEqual(stat.loc[False].values[0], 5601)
self.assertEqual(stat.loc[True].values[0], 4399)
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 testApply(self):
ex = flow.ChannelStatisticOp(name="ByDox",
by=['Dox', 'T'],
channel="Y2-A",
function=len).apply(self.ex)
self.assertIn(("ByDox", "len"), ex.statistics)
stat = ex.statistics[("ByDox", "len")]
self.assertIn("Dox", stat.index.names)
self.assertIn("T", stat.index.names)
def setUp(self):
ImportedDataTest.setUp(self)
self.ex = flow.ChannelStatisticOp(name="ByDox",
by=['Dox', 'Well'],
channel="Y2-A",
function=flow.geom_mean).apply(
self.ex)
self.view = flow.BarChartView(statistic=("ByDox", "geom_mean"),
variable="Well",
huefacet="Dox")
def testSubset(self):
ex = flow.ChannelStatisticOp(name="ByDox",
by=['T'],
channel="Y2-A",
subset="Dox == 10.0",
function=len).apply(self.ex)
stat = ex.statistics[("ByDox", "len")]
from_df = ex.data.groupby(["T", "Dox"]).size()
self.assertEqual(stat.loc[False], from_df.loc[False, 10.0])
self.assertEqual(stat.loc[True], from_df.loc[True, 10.0])
self.assertEqual(stat.loc[False], 5601)
self.assertEqual(stat.loc[True], 4399)
def testBarChart(self):
import numpy as np
ex2 = flow.ChannelStatisticOp(name="Stats1D",
by=["Dox"],
channel="V2-A",
function=np.mean).apply(self.ex)
warnings.filterwarnings(
'ignore',
'axes.color_cycle is deprecated and replaced with axes.prop_cycle')
flow.BarChartView(statistic=("Stats1D", "mean"),
variable="Dox").plot(ex2)
def testBadErrorStat(self):
self.ex = flow.ChannelStatisticOp(name="ByDox_BAD",
channel="Y2-A",
by=['Dox'],
function=flow.geom_sd_range).apply(
self.ex)
self.view = flow.Stats1DView(statistic=("ByDox", "geom_mean"),
error_statistic=("ByDox_BAD",
"geom_sd_range"),
variable="Dox",
huefacet="T")
self.assertRaises(util.CytoflowViewError, self.view.plot, self.ex)
def testBadYErrorStatistic(self):
self.ex = flow.ChannelStatisticOp(name = "V_bad",
channel = "V2-A",
by = ['Well'],
function = flow.geom_sd_range).apply(self.ex)
self.view = flow.Stats2DView(xstatistic = ("Y", "geom_mean"),
x_error_statistic = ("Y", "geom_sd_range"),
ystatistic = ("V", "geom_mean"),
y_error_statistic = ("V_bad", "geom_sd_range"),
variable = "Dox",
huefacet = "Well")
self.assertRaises(util.CytoflowViewError, self.view.plot, self.ex)
def testStats1D(self):
import numpy as np
ex2 = flow.ChannelStatisticOp(name="Stats1D",
by=["Dox"],
channel="V2-A",
function=np.mean).apply(self.ex)
flow.Stats1DView(statistic=("Stats1D", "mean"),
variable="Dox").plot(ex2)
flow.Stats1DView(statistic=("Stats1D", "mean"),
variable="Dox",
variable_scale="log",
scale="logicle").plot(ex2)
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)
