def __init__(self):
SampleStat.__init__(self)
self.type2gene2clones = {}
self.type2gene2reads = {}
types = ['v', 'd', 'j', 'vj', 'dj']
for type in types:
self.type2gene2clones[type] = {}
self.type2gene2reads[type] = {}
def __init__(self, v2freq, j2freq, len2freq, color, marker, name):
SampleStat.__init__(self)
self.type2gene2clones = {}
self.type2gene2clones['v'] = v2freq
self.type2gene2clones['j'] = j2freq
self.len2clones = len2freq
self.color = color
self.marker = marker
self.name = name
def __init__(self, freqs=[]):
SampleStat.__init__(self)
if freqs:
self.freqs = freqs
else:
#self.freqs = [0, 0.001, 0.01, 0.1, 1]
self.freqs = [0, 0.00001, 0.0001, 0.001, 0.01]
self.numclones = [0.0] * len(self.freqs)
self.counts = [0.0] * len(self.freqs)
self.topfreqs = [] # frequencies of the top clones
self.numclones_cumul = self.numclones # cumulative
self.counts_cumul = self.counts # cumulative
self.topfreqs_cumul = [] # cumulative freqs of top clones
def __init__(self):
SampleStat.__init__(self)
#self.numclone = None
# R vegan: diversity
self.simpson = None
self.invsimpson = None
self.shannon = None
self.fisher_alpha = None
# Standard deviation
self.numclone_std = None
self.simpson_std = None
self.invsimpson_std = None
self.shannon_std = None
self.fisher_alpha_std = None
def __init__(self):
SampleStat.__init__(self)
self.len2clones = {}
self.len2reads = {}
self.median_clones = None # median cdr3 length based on # clones
self.median_reads = None # median cdr3 length based on # reads