cospar.simulate.linear_differentiation_model

cospar.simulate.linear_differentiation_model(Nt1=400, progeny_N=1, L=100, diff_sigma=0.5, dL=1, display=1, always_simulate_data=0, used_clone_N=100)

Simulate linear differentiation corrupted with barcode collision (See Fig. 3a)

Parameters

Nt1

Number of initial cell states. They are randomly sampled along the differentiation manifold. Default 400.

progeny_N

Number of progeny for each initial cell state

L

The total progression length.

diff_sigma

Differentiation noise.

dL

Unit progression in a single step

display

Plot figures or not

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.