scPhyloX.tools.data_factory

Attributes

population_size
tumor_data
tumor_size

Functions

cell_number_calc(w, l, r[, coef])	Calculate tumor cell number with given width, height and scale
get_branchlen([seqtab, sys])	Calculate LP distance with given mutation character matrix
get_mutnum([seqtab, sys, filter_trunk])	Calculate LR distance with given mutation character matrix
mutnum_fly(seqs, ref)	calculate LR distance for SMALT-fly dataset
branchlen_fly(seqs, ref[, rs])	calculate LP distance for SMALT-fly dataset

Module Contents

population_size

cell_number_calc(w, l, r, coef=100000000.0)

Calculate tumor cell number with given width, height and scale

Args:

w:

width

l:

heigth

r:

scale

coef:

cell density

Return:

float:

cell number

tumor_data

tumor_size

get_branchlen(seqtab: numpy.ndarray = None, sys=None)

Calculate LP distance with given mutation character matrix

Args:

seqtab:

mutation character matrix

sys:

Gillespie simulator with results

Return:

np.array:

LP distance

get_mutnum(seqtab=None, sys=None, filter_trunk=True)

Calculate LR distance with given mutation character matrix

Args:

seqtab:

mutation character matrix

sys:

Gillespie simulator with results

filter_trunk:

Filter trunk mutations

Return:

np.array:

LR distance

mutnum_fly(seqs, ref)

calculate LR distance for SMALT-fly dataset

Args:

seqs:

DNA muataion character matrix

ref:

reference seuence

Return:

np.array:

LR distance

branchlen_fly(seqs, ref, rs=1)

calculate LP distance for SMALT-fly dataset

Args:

seqs:

DNA muataion character matrix

ref:

reference seuence

rs:

resampling ratio

Return:

np.array:

LP distance