lineage.states.StateDistributionGaPhs
State distribution class for separated G1 and G2 phase durations as observation.
Classes
For G1 and G2 separated as observations. |
Module Contents
- class lineage.states.StateDistributionGaPhs.StateDistribution(bern_p1=0.9, bern_p2=0.75, gamma_a1=7.0, gamma_scale1=3.0, gamma_a2=14.0, gamma_scale2=6.0)
For G1 and G2 separated as observations.
- Parameters:
bern_p1 (float)
bern_p2 (float)
gamma_a1 (float)
gamma_scale1 (float)
gamma_a2 (float)
gamma_scale2 (float)
- params
- G1
- G2
- rvs(size, rng=None)
User-defined way of calculating a random variable given the parameters of the state stored in that observation's object.
- Parameters:
size (int)
- dist(other)
Calculate the Wasserstein distance between this state emissions and the given.
- dof()
Return the degrees of freedom.
- logpdf(x)
To calculate the log-likelihood of observations to states.
- Parameters:
x (numpy.ndarray)
- Return type:
numpy.ndarray
- estimator(x, gammas)
User-defined way of estimating the parameters given a list of the tuples of observations from a group of cells.
- Parameters:
x (numpy.ndarray)
gammas (numpy.ndarray)
- censor_lineage_array(censor_condition, tree, obs, states, desired_experiment_time=2000000000000.0)
Applies censoring to array representation directly.
- Parameters:
censor_condition (int)
tree (scipy.sparse.csr_array)
obs (numpy.ndarray)
states (numpy.ndarray)
- Return type:
tuple[scipy.sparse.csr_array, numpy.ndarray, numpy.ndarray]