Пример #1
0
def concat(fdarray):
    """Merge FlowData together
	"""

    pd_data = [fd.panda for fd in fdarray]
    new_panda = pd.concat(pd_data)
    md = fdarray[0]._metadata
    # Clean up the metadata
    md['$FIL'] = 'merged data'
    newfd = FlowData(panda=new_panda, metadata=md)

    return newfd
Пример #2
0
import numpy as np
from flowdata import FlowData
import matplotlib.pyplot as plt

fd = FlowData('test.fcs')

print fd.markers
(xgrid,den) = fd.histogram(5)

print xgrid
print den

fig, ax = plt.subplots()

ax.semilogy(xgrid,den)
plt.show()
Пример #3
0
#!/usr/bin/env python
# vim: tabstop=8 expandtab shiftwidth=4 softtabstop=4
from timeit import Timer
from flowdata import FlowData
import pandas as pd
import numpy as np


fd = FlowData('test.fcs')
print fd.tags
print fd.markers

print len(fd.CD45)

print fd.get('TIM-3')

data = fd._data
x = fd.get('TIM-3')
y = fd.get('CD45')

i = y > 10
print len(i)
print data[:,y>10]

numpy_select = Timer("""x = fd.get('TIM-3'); y = fd.get('CD45'); x[y>10]""",setup="""from flowdata import FlowData; fd = FlowData('test.fcs'); """)

it = 1000
print "Time per select (Numpy) {} ms".format(numpy_select.timeit(it)/it*1000)

df = pd.DataFrame({'TIM-3':x, 'CD45':y})
#print df
Пример #4
0
#! /opt/local/bin/python
from flowdata import FlowData

fd = FlowData('test.fcs')
fd.tsne('visne', sample = 100)
fd.write('test_write.fcs')

#fcs.write('test_write.fcs',data, metadata)