cospar.simulate.bifurcation_model

cospar.simulate.bifurcation_model(progeny_N=2, t1=5, p1=0.5, p2=1, M=50, L=10, diff_sigma=0.5, repeat_N=1, dL=1, no_loss=False, always_simulate_data=0)

Simulate bifurcation corrupted with clonal dispersion (See Fig. 3e)

Parameters

progeny_N

Fold change of clone size after each generation. 2 means that it will double its clone size after one generation.

t1

Initital sampling time point. Unit: cell cycle. By default t2=t1+1.

p1

Probability to sample cells at t1

p2

Probability to sample cells at t2

M

Total number of clones to simulate

L

Total length of the 1-d differentiation manifold

diff_sigma

Differentiation noise

dL

Step size of differentiation for one generation

no_loss

whether the sampling kills the cell or not. Default: sampling kills cells. x_t0: List of inititial cell locations at t0 along a 1-d line with length L

always_simulate_data

Simulate new data (do not load pre-saved datasets)

Returns

adata – An adata object with clonal matrix, time info etc. Ready to be plugged into CoSpar.