def svilen(self, id=None, *args, **kwargs):
from pyqlb.nstats.well import accepted_peaks
from pyqlb.nstats.peaks import cluster_2d, peak_times, fam_widths
from pyqlb.factory import QLNumpyObjectFactory
from qtools.lib.mplot import svilen, cleanup, render as plt_render
qlwell = self.__qlwell_from_threshold_form(id)
self.__set_threshold_context(qlwell)
well_path = self.__well_path()
# oh shit
factory = QLNumpyObjectFactory()
raw_well = factory.parse_well(well_path)
crap, crap, gold, crap = cluster_2d(accepted_peaks(qlwell), c.fam_threshold,
c.vic_threshold)
times = peak_times(gold)
widths = fam_widths(gold)
title = "VIC+/FAM- droplet traces (accepted events)"
ranges = [(int(t-(w*2)), int(t+(w*2))) for t, w in zip(times, widths)]
if c.fam_threshold == 0 or c.vic_threshold == 0:
ranges = []
title = "%s (no events in quadrant)" % title
elif len(ranges) > 100:
ranges = ranges[:100]
title = "%s (truncated at first 100)" % title
fig = svilen(title, raw_well.samples, ranges, widths)
response.content_type = 'image/png'
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def well_fragmentation_probability(well):
"""
Returns the percentage likelihood per droplet that the molecules in
the two channels are unlinked (TODO: refine definition)
Returns the 3-tuple (probability, ci_low, ci_high). If thresholds are
not present, then the function will return the 3-tuple (None, None, None)
"""
from qtools.lib.nstats.frag import prob_of_frag
fam_threshold = well.channels[0].statistics.threshold
vic_threshold = well.channels[1].statistics.threshold
if not (fam_threshold and vic_threshold):
return (None, None, None)
ok_peaks = accepted_peaks(well)
fampos_vicpos, fampos_vicneg, famneg_vicpos, famneg_vicneg = \
cluster_2d(ok_peaks, fam_threshold, vic_threshold)
retarr = prob_of_frag(len(fampos_vicneg), len(fampos_vicpos),
len(famneg_vicneg), len(famneg_vicpos),
len(ok_peaks))
if not retarr:
return (None, None, None)
else:
pct_interval, vic_interval, fam_interval, linked_interval = retarr
return pct_interval
def pos_cluster_angle_2d(qlwell, fam_threshold=None, vic_threshold=None):
if fam_threshold is None:
fam_threshold = qlwell.channels[0].statistics.threshold
if vic_threshold is None:
vic_threshold = qlwell.channels[1].statistics.threshold
ok_peaks = accepted_peaks(qlwell)
fampos_vicpos, fampos_vicneg, famneg_vicpos, famneg_vicneg = \
cluster_2d(ok_peaks, fam_threshold, vic_threshold)
if len(fampos_vicneg) == 0 or len(famneg_vicpos) == 0 or len(fampos_vicpos) == 0:
return 0
return cluster_angle_ccw(fampos_vicpos, fampos_vicneg, famneg_vicpos)
