def quartile_concentration_ratio(well, channel_num=0, threshold=None, peaks=None, min_events=4000):
if peaks is None:
peaks = accepted_peaks(well)
if len(peaks) < min_events:
return None
if not threshold:
threshold = well.channels[channel_num].statistics.threshold
if not threshold:
return None
quartile_size = len(peaks)/4
first_quartile = peaks[0:quartile_size]
last_quartile = peaks[len(peaks)-quartile_size:]
first_pos, first_neg = cluster_1d(first_quartile, channel_num, threshold)
fq_conc = concentration(len(first_pos), len(first_neg), droplet_vol=well.droplet_volume) # could be nan
last_pos, last_neg = cluster_1d(last_quartile, channel_num, threshold)
lq_conc = concentration(len(last_pos), len(last_neg), droplet_vol=well.droplet_volume) # could be nan
# if conc is nan or zero, we can't compute a real ratio
if math.isnan(fq_conc) or math.isnan(lq_conc) or fq_conc == 0 or lq_conc == 0:
return None
else:
return lq_conc/fq_conc
def well_statistics(qlwell, override_thresholds=None):
from pyqlb.nstats import concentration, concentration_interval
from pyqlb.nstats.peaks import cluster_1d
from pyqlb.nstats.well import well_observed_positives_negatives, accepted_peaks
if override_thresholds is None:
override_thresholds = [None]*len(qlwell.channels)
wellui = WellStatisticsUI(channels=[])
for idx, channel in enumerate(qlwell.channels):
if not override_thresholds[idx]:
positives, negatives, unclassified = well_observed_positives_negatives(qlwell, idx)
threshold = channel.statistics.threshold
conc = channel.statistics.concentration
conc_interval = (channel.statistics.concentration,
channel.statistics.concentration_lower_bound,
channel.statistics.concentration_upper_bound)
else:
positives, negatives = cluster_1d(accepted_peaks(qlwell), idx, override_thresholds[idx])
threshold = override_thresholds[idx]
conc = concentration(len(positives), len(negatives), qlwell.droplet_volume)
conc_interval = concentration_interval(len(positives), len(negatives), qlwell.droplet_volume)
channelui = WellChannelStatisticsUI(positives=len(positives),
negatives=len(negatives),
threshold=threshold,
concentration=conc,
concentration_interval=conc_interval)
wellui.channels.append(channelui)
return wellui
