scPhyloX.simulation.tissue

Classes

Reaction	Cell division/differentiation type
Cell	Cell class
System	Gillespie simulation

Functions

bt(t, a, b, k, t0)
cellnumber(t, xx, a, b, k, t0, p, r, d)
simulation(x0, max_t, mut_rate, a, b, p, r, k, d, t0)	Run gillespie simulation in tissue development model

Module Contents

bt(t, a, b, k, t0)

cellnumber(t, xx, a, b, k, t0, p, r, d)

class Reaction(rate=0.0, num_lefts=None, num_rights=None, index=None)

Cell division/differentiation type

Args:

rate:

reaction rate function

num_lefts:

Cell numbers before reaction

num_right:

Cell numbers after reaction

index:

Reaction index

rate = 0.0

num_lefts

num_rights

num_diff

index = None

combine(n, s)

propensity(n, t)

class Cell(seq=None, gen=None, cellid=None, celltype=None, is_alive=True, lseq=1500, init=False)

Cell class

Args:

seq:

DNA sequence

gen:

Cell generation

cellid:

Cell id

celltype:

Cell type, stem/non-stem cell

is_alive:

Is cell alive or died

lseq:

Length of DNA seq

init:

if init, cell will generate DNA seq with given length lseq automatically

seq = None

gen = None

celltype = None

lseq = 1500

cellid = None

is_alive = True

initialize(lseq)

Generate DNA seq with given length lseq

class System(num_elements, inits=None, nbase=1500, mut_rate=1, mut_rate1=None, max_t=35, start_t=0)

Gillespie simulation

Args:

num_elements:

Cell type number

inits:

Initial cell number

nbase:

length of cell DNA seq

mut_rate:

mutation rate of DNA seq, follows Poisson distribution

max_t:

maximum simulation time

start_t:

Mutate start time

num_elements

reactions = []

start_t = 0

max_t = 35

mut_rate = 1

global_id

Stemcells

Diffcells

mut_num = 0

cell_num

mut_time = []

mut_num_SC

mut_num_DC

log_cells

lineage_info

add_reaction(rate=0.0, num_lefts=None, num_rights=None, index=None)

Add reactions to simulation

Args:

rate:

reaction rate function

num_lefts:

Cell numbers before reaction

num_right:

Cell numbers after reaction

index:

Reaction index

mutate(cell, mutrate)

simulation DNA mutation

Args:

cell:

cell

mutrate:

mutation rate

Return:

cell:

cell with mutated DNA seq

stemrenewal()

stem cell -> 2 stem cells

stemdiff()

stem cell -> non-stem cell + non-stem cell

diffdeath()

non-stem cell -> death cell

stemasym()

stem cell -> stem cell + non-stem cell

evolute(steps)

simulation(x0, max_t, mut_rate, a, b, p, r, k, d, t0, mut_rate1=None)

Run gillespie simulation in tissue development model

Args:

x0:

initial cell number

max_t:

stop time

mut_rate:

mutation rate

a,b,p,r,k,d,t0:

paras

Return:

Object:

gillespie simulator with results