phylovelo.gene_expr

Module Contents

Classes

Gene	Gene class
GeneExpr	Gene expression program

class Gene(mu0: float, drift: float, sigma: float = None, t0: int = 0)

Gene class

Args:

mu0:

Initial expression

drift:

Drift coefficient of DP

sigma:

Diffusion coefficient of DP

t0:

Gene initial time

diffusion()

Diffusion one step.

base_expr_calc(t: int)

Calculate base expression

Args

t:

time

Return:

Base expression at time t

class GeneExpr(Ngene: int, r_variant_gene: float, diff_map: dict, state_time: dict, forward_map: dict = None)

Gene expression program

Args:

Ngene:

Gene number

r_variant_gene:

Ratio of gene changes with differentiation

diff_map:

Differentiation relationships between different cell types {a:[b,c]} means ‘a’ is differentiated from ‘b’ and ‘c’

state_time:

Pseudo time of each states

forward_map:

Only use in convergent model simulation {a:b} means ‘a’ will differentiated to ‘b’

generate_genes(mu0_loc: float = 20, mu0_scale: float = 3, drift_loc: float = 0, drift_scale: float = 1)

Generate genes

Args:

mu0_loc:

Mean of initial expression

mu0_scale:

Variation of initial expression

drift_loc:

Mean of gene drift

drift_scale:

Variation of drift

expr(state, time)